On Tuesday Fonseka appeared before a separate military tribunal over charges that he illegally engaged in politics while head of the Sri Lankan armed forces.
According to Anura Dissanayake, a local politician and Fonseka ally, the former military chief objected to the court martial soon after it began, saying the presiding panel of three officers was biased because it included two men whom he previously disciplined when he was head of the army.
The panel's third member was a close relative of the current army commander who initiated the court-martial, Dissanayake said.
Fonseka's arrest has been condemned by Sri Lanka's opposition and human rights groups, who accuse the government of retaliating against a man who dared challenge Mahinda Rajapaksa, the country's president, in his bid for re-election.
As Tuesday's first court martial began, police clashed with Fonseka supporters at a protest calling for his release in the town of Pandura, south of the capital, Colombo.
Opposition groups said at least 14 people were arrested and two others hospitalised after being beaten, with police firing tear gas to break up the demonstration.
Police have made no official comment on the incident.
Soon after Fonseka's arrest on February 8, government officials went public with various allegations against him, including that he plotted to assassinate Rajapaksa and seize power in a coup.
Neither of those allegations have been followed up with formal charges.
Despite his detention, Fonseka is running for a seat in parliamentary elections scheduled for April 8.
He has denied all the charges against him saying they have been fabricated by officials in Rajapaksa's administration to silence him.
The court martial process itself been shrouded in secrecy with the military barring reporters from proceedings and refusing to release any details.
If convicted of the charges, he could reportedly face up to five years in jail.
Former close allies, Rajapaksa once referred to Fonseka as a "national hero" for his role in leading the Sri Lankan military in its final victory over Tamil Tiger rebels.
The defeat of the Tigers in May last year brought an end to more than two decades of bloody civil war.
But the two men fell out shortly after over who should take credit for the victory.