Fonseka, a war hero last year after helping end the Indian Ocean nation's 37-year civil war, stepped down as army chief in November and unsuccessfully challenged Rajapakse, his former boss and ally, in January elections.
He faced a three-member panel on Tuesday at the beginning of a court martial on a charge of illegally engaging in politics while serving in the military. He faces a parallel charge of making irregular military procurements.
"The legal team raised preliminary objections to the panel because all three military judges were seen as biased against General Fonseka," the retired general's spokesman Anura Kumara Dissanayake told AFP.
"We also argued that the court martial had no jurisdiction over the retired officer," he said, adding that a hearing for the procurement charge would begin on Wednesday.
Fonseka says the accusations are politically-motivated and part of a vendetta designed to stop him campaigning for parliamentary elections due on April 8.
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