Fonseka in an address to the Foreign Correspondents' Association in Colombo yesterday also denied that his troops killed Balachandran, the 12-year-old son of slain LTTE chief Velupillai Prabhakaran.
Britain's Channel 4 television network last month released new photographs of what they called Balachandran inside a military bunker having a snack and another frame which showed his bullet riddled body.
"These pictures could have been doctored," Fonseka said.
"The bunker where he was looks too tidy and orderly to be one of our bunkers. In the battle field, we did not have the luxury of having such neat and tidy bunkers," Fonseka said.
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However, Fonseka repeated his offer to face any independent international investigation and said it was his "duty" as the commander at the time to face any probe.
He accused the government of not addressing accountability issues and allowing calls for a war crimes probe to escalate without addressing the basic questions many had.
"People want to know what happened. Some want to clear doubts," Fonseka said, adding that he was prepared to answer the charges if he was questioned by any international independent probe.
He suffered a crushing defeat and was later arrested and jailed till May last year when he was freed on a presidential pardon.
Fonseka said Sri Lanka will face more international allegations of war crimes unless it agreed to a probe.