The general was arrested by the army last month on the orders of Rajapaksa.
The president appointed a three-member tribunal to try Fonseka for participating in politics while in office and violating military procurement procedures.
Rajapaksa and Fonseka had been allies in the successful offensive that ended the country's 25-year civil war against the Tamil Tiger rebels, but they split following the end of the conflict last May.
Sri Lankan officials have said "due process" would be followed in dealing with Fonseka, and have argued that "no one is above the law".
Last month Fonseka's wife petitioned the supreme court, calling for the general's arrest to be ruled illegal.