Three Tamil Tiger rebel leaders who tried to surrender during the bloody climax of Sri Lanka's civil war in May were shot and killed on the orders of the country's defence minister and a senior adviser to President Mahinda Rajapaksa, the army commander at the time has claimed.

General Sarath Fonseka, who helped direct the final offensive against the Tigers but later broke with the government and is running for president in next month's elections, said he had been personally unaware of the Tamils' attempts to give themselves up, which included frantic last-minute appeals for help to a Norwegian minister, diplomats, journalists and UN and Red Cross officials.

"Later I learned that Basil [Rajapaska, a senior presidential adviser] had conveyed this information to the defence secretary, Gothabaya Rajapaksa, who in turn spoke with Brigadier Shavendra Silva, commander of the army's 58th division, giving orders not to accommodate any [Tiger] leaders attempting surrender and that they must all be killed," Fonseka told the pro-opposition Sunday Leader newspaper in Colombo.

Fonseka said Balasingham Nadesan, head of the Liberation Tigers of Tamil Eelam's political wing, Seevaratnam Puleedevan, head of the group's peace secretariat, and a Tiger leader known as Ramesh had been assured through intermediaries by Basil Rajapaksa and Gothabaya Rajapaksa, brothers of the president, that they would be given safe conduct.

According to subsequent accounts, the men were advised: "Get a piece of white cloth, put up your hands and walk towards the other side in a non-threatening manner."

"It [the surrender method] was their idea," Fonseka told the newspaper, referring to Basil and Gothabaya Rajapaksa.

When the three men approached government lines some time after midnight on 17 May they walked into a trap, Fonseka suggested. Troops opened fire with machine guns, killing all three and a number of family members.

A Tamil eyewitness account said Nadesan's wife, a Sinhalese, called in Sinhali to the soldiers: "He is trying to surrender and you are shooting him." She also died in the hail of bullets.

Faced by government denials and threats of legal action today, Fonseka appeared to backtrack, claiming the newspaper reported his remarks out of context. "They (army soldiers) never committed any criminal act. There was no attempt at surrender on May 17, 18 and 19," he said. He would take full responsibility for any human rights violations during the final stages of the war. Despite disavowing his earlier remarks, Fonseka's claims about the circumstances surrounding the three men's deaths resemble contemporaneous reports in regional and western media, including the Guardian, that were denied by the Sri Lankan government.

Fonseka's whereabouts during the incident was also a matter of confusion. He told a press conference in Colombo on Sunday that he was in China. It was unclear how this statement could be reconciled with his appearance on Sri Lankan state television on 18 May to proclaim victory over the Tigers and confirm that their leader, Velupillai Prabhakaran, had been killed. "We can announce very responsibly that we have liberated the whole country from terrorism," Fonseka told Rupavahini television.

Fonseka's role in the war made him a hero for many Sinhalese, a factor that may have hastened his rupture with President Rajapaksa. He was removed as army commander two weeks after the war concluded. His claims about what happened last May, and subsequent backtracking, will be viewed in the context of his presidential campaign.

Sri Lanka denies responsibility for the three men's deaths. Officials have suggested the Tamil leaders were killed by their own side, after they decided to surrender.

Responding to Fonseka, Mahinda Samarasinghe, the human rights minister, said: "The government totally denies this allegation … We reject this malicious allegation against our heroic soldiers." Offering yet another version of events, he said the rebels were carrying white flags in an attempt to fool the army and were not trying to surrender.

Basil Rajapaksa told the Sunday Leader he had not been contacted by a Norwegian intermediary over the surrender offer. Gothabaya Rajapaksa and Brigadier Silva have not commented in public on Fonseka's claims.

Sri Lanka's conduct of the final phases of the war, in which up to 20,000 people may have died, its subsequent internment of an estimated 270,000 Tamil civilians, and violence against government critics, including last January's assassination of the Sunday Leader's former editor, Lasantha Wickrematunge, have provoked widespread condemnation by human rights groups, NGOs and some western governments. But calls by Amnesty International and others for an independent investigation by the UN or another independent body have so far been blocked.

Fonseka's allegations echo a report published in June by a Sri Lankan human rights group, University Teachers for Human Rights (Jaffna), that cited army sources in stating that a "politically ordered massacre of people who wanted to surrender or surrendered" had taken place. The group also reported widespread killings by rebels of Tamil civilians who were fleeing the war zone.

The report said: "The army had for the most part conducted itself in a disciplined manner in trying to protect civilians. But once the command gives a signal for barbarity to be let loose, the men touch the most depraved depths of humanity."

Tamer of the Tigers

Widely seen as the architect of Sri Lanka's military success against the Tamil Tigers, General Sarath Fonseka is credited with eliminating the separatist group's leadership and ending a war that began in 1983 and killed more than 70,000 people.

Born in 1950, the general started his career in the Sri Lankan army in 1970. His training took him all over South Asia as well as to the US and the UK.

He rose through the ranks and became known as a tough commander not afraid to join in with action against the Tigers. He was wounded in 1993 and almost killed by a suicide bomber in 2006.

His role in Operation Riviresa in 1995 – when the army captured the town of Jaffna from the rebels – was one of the high points of his career.

One of his biggest setbacks occurred in 2000 when the Tigers managed to gain control of the strategically important Elephant Pass, one of the few routes leading to the Jaffna peninsula. His troops recaptured it in January this year.

Last July Fonseka was appointed as Sri Lanka's first chief of defence staff. He resigned last month, feeling that he had not receive the recognition he deserved for the war victory.

Fonseka is to run as the People's Liberation Front presidential candidate in the general election, scheduled for 26 January. He has pledged to abolish the powerful executive presidency and return power to parliament in six months, and to take measures to curb corruption and restore democracy.

Fifteen opposition parties – all with little hope of defeating the incumbent, Mahinda Rajapaksa, on their own – have previously said they would support Fonseka in the election.

The general's relationship with the government has become increasingly bitter in recent weeks.