President Mahinda Rajapaksa signed papers ordering the release of Sarath Fonseka and handed them over to his chief of staff Saturday before embarking on an official visit to Qatar, presidential spokesman Bandula Jayasekara said Sunday.
The papers will be sent to the Justice Ministry on Monday, Jayasekara said.
Rajapaksa's move came after Foreign Minister G.L. Peiris met with Secretary of State Hillary Rodham Clinton on Friday in Washington, with the protection of human rights highlighted in their meeting. The U.S. has called Fonseka a political prisoner.
Fonseka is serving a 30-month jail term after a court-martial found him guilty of planning his political career while still in the military and of committing fraud in purchasing military equipment.
Separately, in November 2011, he was sentenced to an additional three-year prison term for implicating the defense secretary and president's brother Gotabhaya Rajapaksa in war crimes during Sri Lanka's civil war. He has appealed that conviction.
Fonseka has said the cases are a political vendetta launched to persecute him for daring to run against Rajapaksa in the 2010 election. The government has denied any political motive for the legal action.
The details of Fonseka's release—including when he will be freed and whether the release applies to all his cases—were not immediately clear. According to Sri Lankan law, a person convicted of a crime and sentenced to a jail term of at least six months cannot contest elections for seven years. A full presidential pardon could restore those rights.
Government spokesmen over the past few days have been hinting that Fonseka will be given a full pardon. Rajapaksa also got approval from his Cabinet for Fonseka's release, according to a government website.
Fonseka was hailed as a war hero in 2009 after he led Sri Lanka's army to victory in its 26-year civil war with separatist Tamil Tiger rebels, and both he and Rajapaksa were immensely popular among the Sinhalese majority for defeating a rebel group that had seemed invincible for decades.
But the two men had a falling out months after the war ended, and their relationship deteriorated further after the general challenged Rajapaksa in the Jan. 26, 2010, election. Fonseka was arrested about two weeks later.
Later that year, a court-martial convicted him and stripped him of his title, medals, pension and other honors, and dishonorably discharged him from the army.
While in detention, Fonseka won a parliamentary seat on the opposition ticket in April 2010, but he was disqualified from holding office after the court-martial.
During her meeting with Peiris on Friday, Clinton discussed a range of topics, including accountability issues in the island nation's civil war and ethnic reconciliation. Clinton "also stressed ... the importance of protection of human rights," State Department spokeswoman Victoria Nuland said.
Sri Lanka has faced growing criticism over alleged rights abuses in the final phase of the civil war. Its ties with Washington have been strained by U.S. sponsorship of a resolution passed by the U.N. Human Rights Council in March to press Sri Lanka to conduct an independent probe into civilian deaths in the final months of the war.
The conflict that killed more than 80,000 people ended in May 2009, when government forces crushed the rebels who had fought for a separate state for ethnic minority Tamils, claiming decades of discrimination by the Sinhalese majority.