The papers will be sent to the Ministry of Justice on Monday, Jayasekera said.
Fonseka unsuccessfully tried to unseat Rajapakse in the January 2010 presidential election. The two fell-out as to who should take credit to crush the Tigers in May 2009, that ended nearly four-decades of bloodshed.
Rajapakse on Thursday announced intentions to pardon his erstwhile military chief-turned main political foe, Fonseka.
On Friday, high court imposed one million rupee bail (8,000 dollars) on Fonseka in a case where he is accused of employing military deserters, his lawyer Saliya Peiris said. However, it was not immediately clear if Fonseka would have to stand trial for the offence.
The government detained Fonseka two weeks after his election defeat in February 2010, on charges of corruption relating to military purchases. He was convicted given a 30-month jail sent