By Trinna Leong and Al-Zaquan Amer Hamzah
KUALA LUMPUR, Feb 10 (Reuters) - Malaysia's highest court rejected on Tuesday an appeal by opposition leader Anwar Ibrahim against a sodomy conviction, sending the politician who poses the greatest threat to the long-ruling coalition back to prison for five years.
The U.N. Human Rights office and Australia said they were disappointed by the ruling. Human Rights Watch condemned it as persecution and Amnesty International said it would have a chilling effect on freedom of expression.
Anwar, the ruling party's rising star in the mid-1990s before he fell out with then Prime Minister Mahathir Mohamad, denied the charge that led to his second conviction for sodomy as a fabrication aimed at ending his political career.
"I will walk again for the third time into prison but rest assured that I will walk in with my head held high," a defiant Anwar said in a statement he read out in court.
"I maintain my innocence."
Prime Minister Najib Razak's government has rejected any suggestion of interference in the case.
"Malaysia has an independent judiciary, and there have been many rulings against senior government figures," the government said in a statement after the ruling.
The United States said it was "deeply disappointed" with the conviction. "The decision to prosecute Mr. Anwar and the conduct of his trial have raised a number of serious concerns about rule of law and the fairness of the judicial system in Malaysia," National Security Council spokeswoman Bernadette Meehan said.
Anwar criticized the court saying that in rejecting his appeal it was "bowing to the dictates of the political masters."
"You chose to remain on the dark side and drown your morals and your scruples in a sea of falsehood and subterfuge," he told the judges who walked out of the court as he spoke.
"I will not surrender," he said.
Anwar later comforted his wife and children and had a meal with them before being taken to the Sungai Buloh prison, about 30 km (20 miles) from Kuala Lumpur.
A court found the 67-year old former deputy prime minister guilty in March last year of sodomizing a former political aide.
The conviction disqualifies him from political office and contesting the next election that must be held by 2018.
Nurul Izzah, Anwar's daughter who is also a political leader in his Parti Keadilan Rakyat, was also defiant.
"This is not the end," said told reporters outside the court.
Anwar is head of a three-party opposition alliance that made stunning gains in a 2013 general election which for the first time raised the possibility of a genuine challenge for the coalition that has ruled Malaysia since independence in 1957.
The decision against him raises the prospect of a fresh bout of political agitation which could make investors even more cautious about putting money into an economy so heavily dependent on oil and gas revenues at a time when global prices are so low.
Anwar's party and the opposition alliance plan protests against the verdict. Hundreds of his supporters outside the court waved party flags and shouted "Down with Barisan Nasional," referring to the ruling coalition.
"What has happened today is not fair but this has happened before ... we will keep fighting," said an Anwar supporter who identified herself as Salihah M, 36.
Australia said it was disappointed and "deeply concerned" about Anwar's sentence.
Phil Robertson, deputy Asia director for Human Rights Watch, called the court ruling a "travesty of justice."
"Prime Minister Najib Razak's government has persisted in its politically motivated prosecution of opposition leader Anwar Ibrahim at the expense of democratic freedoms and the rights to non-discrimination and privacy for all Malaysians," he said.
The U.N. Human rights office said sodomy should not be a criminal offense.
Anwar has for years been the greatest threat to Malaysia's political establishment. His jailing could undermine the opposition's unity and the challenge it poses but it could also galvanize dissent.
His political career has been turbulent since he was sacked in 1998 after falling out with then premier Mahathir and then campaigned against corruption and nepotism and led a nationwide "reformasi" (reform) protest movement.
He has been beset by legal problems and spent several years in prison after being convicted of corruption and an earlier sodomy charge.
Mahathir remains hugely influential and his old guard was critical of an attempt by Prime Minister Najib to introduce reforms after he came to power in 2009.
Following the ruling coalition's worst ever election result, in the 2013 polls, Mahathir attacked what he called Najib's "bad performance."
Some ruling party members and analysts have played down fear of upheaval in response to Anwar's return to jail.
"Anwar's political image is not anywhere near close to what it was in the '90s," Wan Saiful Wan Jan, of the Institute for Democracy and Economic Affairs, said earlier.
"The country has moved on." (Additional reporting by Doina Chiacu in Washington; Writing by Praveen Monon; Editing by Robert Birsel)
This was Anwar's final appeal, and once the proceedings ended he was led by police out of the court, presumably to immediately start serving time on charges of sodomizing a then 23-year-old aide who worked in his office.
"I have to go. Time's up," the 67-year-old politician told his supporters inside the court. "I will miss you all," he said bowing to them before walking out.
Anwar was accused of sodomizing Saiful Bukhari Azlan, who was working as a lowly functionary in the opposition election campaign office, in 2008. Anwar was acquitted by the High Court in 2012 but the Appeals Court overturned the acquittal in March last year and sentenced him to five years in prison.
Anwar appealed in Federal Court, which in its Tuesday ruling said there was "overwhelming evidence" to support the conviction. "It is beyond reasonable doubt that (Saiful) was sodomized by the appellant. The appeal is dismissed," said Justice Arifin Zakat, who read the verdict for two hours on behalf of the five-judge panel.
The court also sentenced him to five years imprisonment, even though the prosecutor had asked for more than six years. Sodomy, even consensual, is a crime in Muslim-majority Malaysia and is punishable by up to 20 years in prison. Saiful maintained that he submitted to it because he was afraid of Anwar.
Now 30, Saiful has since got married and has a son. He said on his blog Tuesday he is thankful for the judgment, which proves the court found him a credible witness. "What is important is that I and my family can now move forward," he wrote.
The Federal Court said Anwar's allegations that the case was a political conspiracy "remains an allegation, unsubstantiated by any facts whatsoever." It also rejected the defense argument that the semen samples taken from Saiful's body were tampered with by the police.
Addressing the judges from the dock after the verdict, Anwar said: "You have become partners in crime in the murder of judicial independence," prompting them to get up and walk out of the room, with Justice Arifin heard saying "I don't need to hear all this."
Anwar, however, continued speaking from the dock. "Allah be my witness. I pledge that I will not be silenced. I will fight on for freedom and justice. I will never surrender."
"I maintain my innocence. This to me is a fabrication coming from a political conspiracy to stop my political career," Anwar said.
As the last words of the verdict were read out, Anwar's wife, Wan Azizah, burst into tears. Anwar hugged and consoled her before turning to his children and grandchildren. He smiled and hugged them too.
Watched by about 300 policemen, hundreds of his supporters gathered peacefully outside the imposing court building in Putrajaya, the administrative capital of Malaysia. The supporters are "definitely disappointed," said Edmund Teoh, 29, calling the court partial and unjust.
The verdict is the "death of justice. We will keep on fighting for a better Malaysia. We won't give up," said another supporter, Tey Khang Fai, 33.
In an apparently pre-written statement released minutes after the verdict, the Prime Minister's Office said Anwar's case has gone through an exhaustive legal process, and that the case was brought by an individual, not the government.
"The process is now complete and we call on all parties to respect the legal process and judgment ... Malaysia has an independent judiciary, and there have been many rulings against senior government figures," it said.
Anwar previously was imprisoned for six years after being ousted as deputy prime minister in 1998 on earlier charges of sodomizing his former family driver and abusing his power. He was freed in 2004 after Malaysia's top court quashed that sodomy conviction. That case was also widely seen as politically motivated, as it came at a time when he was locked in a power struggle with then Prime Minister Mahathir Mohamad.
The latest verdict brought forth a torrent of criticism from local and international human rights groups including Amnesty International, Human Rights Watch and International Federation for Human Rights. They called the verdict "disgraceful," a "black day" and "totally unjust."
Malaysian human rights group Suaram pointed out that that the political nature of the trial was apparent from the fact that Saiful had met with the prime minister and senior officials before making a police complaint; medical records had shown no penetration; one of Anwar's lawyers was charged twice with sedition for criticizing the Appeals Court judgment.
"The Federal Court's verdict is the disgraceful conclusion of a relentless judicial campaign against Anwar Ibrahim. Malaysia's judiciary failed to demonstrate its independence from the executive branch in a trial that had clear political motivations," said FIDH President Karim Lahidji.
Anwar said his jailing for a second time would be toughest on his family, but that they were all very supportive.
Instead of breaking up his three-party alliance, he warned Najib that jailing him could backfire and galvanize more support for the opposition.
"They will continue with or without Anwar," Anwar said. "Authoritarian leaders always believe the best way to deal with dissidents is to jail them, but throughout history, it has always backfired," he said.
Anwar led his alliance to unprecedented gains in 2008 elections and made further inroads in 2013 polls. Najib's National Front coalition won with a slimmer majority and lost the popular vote to the opposition.
Associated Press journalists Paul Joshua and Vincent Thian in Putrajaya contributed to this report.