He will answer to nine charges related to financing terrorism, armed robbery, abduction, arson, attempted murder, assault, and battery.
The pardon came after his meeting with his Ethiopian counterpart Sahle-Work Zewde, who is on an official tour of Tanzania.
Nairobi said the fighting is likely to create a security crisis for Kenya.
He was prevented from leaving the premises from January 15 as soldiers and police surrounded the compound.
Executives at Kenya Airways, RwandAir and Uganda Airlines all concede to a challenging business environment.