The fire broke out in an area used to store faulty batteries and other waste products, the company said.
The company tested more than 200,000 phones to discover the problem.
Jay Y. Lee may face several charges, including bribery, over his alleged role in a corruption scandal that could unseat President Park Geun-hye.
Prosecutors are looking into whether Samsung payments were connected to a 2015 decision by the national pension fund to back a controversial merger of two group affiliates.
A software update will disable the smartphones later this month.
The justices sent the case back to a lower court to reassess the proper amount of damages.