Fonseka told the media in Colombo that at most, 4,000 to 5,000 might have died while being in LTTE bunkers, said the website.
He vehemently rejected UN claims that at least 40,000 civilians had been killed in the final stage of the war.
If that claim is true, human bones must be dug up everywhere at Pudukudirippu and Kilinochchi, he said.
According to him, 23,000 LTTE had died, while 12,000 were rehabilitated by the government.
Fonseka also said the ICRC, which had one of its ships anchored in the area during the final two weeks of the war had not confirmed the casualty claim by the UN.
In a June 2009 report, the ICRC said its ‘Green Ocean’ had transported 13,500 patients, injured and others.
Wanni attack and its population
On an order by the government, the UN and other international agencies had vacated the Wanni in September 2008.
The then Mullaitivu district secretary Imelda Sukumar and the statistics received by the LLRC said Pudumathan had 360,000 residents.
Quoting Mannar bishop Rayappu Joseph and Kilinochchi and Mullaitivu DS statistics, the LLRC placed the residents of the Wanni at 429,059.
The government said in April 2009 that around 70,000 lived in the war zone and that more than 280,000 civilians crossed over from LTTE-held areas.
In a January 2012 report, the TNA responded to the LLRC report and said between 75,000 and 146,679 persons were unaccounted for.
Heavy weapons attacks on hospitals
Both Fonseka and Rear Admiral Sarath Fonseka have also admitted the Army attacked hospitals in the no war zones with heavy weapons.
The former has, on several times, expressed willingness to give evidence at an internationally-assisted inquiry into war crimes and human rights violations allegations against the armed forces.