The team said Folger, who was bed-ridden before last month's Japanese Grand Prix when his body effectively shut down, would have to follow a special diet and was now going through a complete detoxification process.
Folger, 24, also missed the races in Australia and Malaysia and will be absent from this weekend's season-ending round in Valencia, Spain.
The rookie, who is still 10th in the standings and is contracted for 2018, is the only German in the top flight of grand prix motorcycling. He finished second in his home race at the Sachsenring in July.
Folger previously suspected Epstein-Barr virus, which can leave the sufferer feeling tired for weeks or months, was the cause of his problems.
"It’s a huge relief that we now have a clear understanding of the situation and how to move forward," said the rider in the team statement.
"The past six weeks have been very difficult for me, not knowing what’s happening or why my body shut down completely," he added.
"I’ve been living with elements of this since 2011 but I’ve always been able to overcome it and we never really knew what it was."
(Reporting by Alan Baldwin in London, editing by William Maclean)
