He has said the government is seeking revenge for his decision to stand against the president and wants to keep him from speaking in parliament.
The first court martial ordered the removal of the medals he had earned during his 40-year military career as well as stripping him of his rank and pension.
He also faces civilian charges of employing army deserters, as well as revealing state secrets -- offences that carry a 20-year jail term.
He has also challenged in the Supreme Court the re-election of Rajapakse.
The 37-year ethnic conflict in Sri Lanka ended in May last year when government forces led by Fonseka wiped out the Tamil Tiger separatist group which had fought since 1972 for a Tamil homeland.
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The United Nations estimates that at least 7,000 ethnic Tamil civilians were killed in the final months of fighting between government troops and the Tamil Tigers. President Mahinda Rajapakse approved the prison sentence for a period of two-and-a-half years after returning Wednesday from N