He made the comment in response to questions raised by journalists at the Colombo high court where he was present for a hearing, BBC Sandeshaya reports.
Gen. Fonseka said he believed the Army did not commit war crimes, but noted it was important to investigate if there is an accountable accusation.
Past experiences
There is no harm of an investigation if a minority in the over 200,000 strong Army has committed even a minor wrong, he said.
He rejected claims by the opposition that the government has agreed for an internal investigation in order to appease the international forces.
Fonseka noted that even in the past, accusations against the Army had been investigated and the culprits brought to book, in instances such as the murders of Premawathi Manamperi, Krishanthi Coomeraswamy and schoolboys of Embilipitiya.
He added that as the former Army commander, he was prepared to face any investigation.