Crew members said Chan made odd gestures before he entered the plane's rear restroom shortly after takeoff and began to scream, according to the complaint.
Chan told the FBI that he "came back to reality" and exited the restroom, at which point the crew noticed his "pants were down, his shirt was untucked and all the compartments in the restroom were opened."
When crew members tried to get Chan to sit, he fought them and had to be subdued in a choke hold, the complaint said.
Chan told agents who interviewed him in Pittsburgh that he ate marijuana cookies while waiting for his flight to depart in Philadelphia.
"Chan advised he has a medical marijuana card and he took double his normal dose," the complaint said.
Margaret Philbin, a spokeswoman for the U.S. attorney's office in Pittsburgh, said Chan has a legally issued medical marijuana card for a "legitimate" health issue, which she declined to identify.
The flight was diverted to Pittsburgh International Airport, where Chan was arrested, then jailed until a federal magistrate granted him bond Tuesday, Philbin said.
Chan remained jailed Wednesday because Allegheny County officials have also charged him with disorderly conduct, Philbin said.
Chan arrived at Philadelphia International Airport after attending a conference in the Dominican Republic. The flight to Los Angeles was part of his trip home to San Francisco, authorities said.
Chan was scheduled for a preliminary hearing Wednesday afternoon, but that was postponed until Friday because of a paperwork delay, Philbin said.
The charge of interfering with the duties of a flight attendant carries up to 20 years in prison and a $250,000 fine.