The President, who took power in 2005, is seeking a third term in office, two years ahead of completing his second term.
Cabinet spokesman and Minister Keheliya Rambukwella said Rajapaksa had been nominated by the ruling Sri Lanka Freedom Party (SLFP), according to reports.
He said the SLFP was unanimous in its decision despite opposition from some coalition members. The National Heritage Party had this week quit the government in protest against holding the election next year before implementing key constitutional changes.
Sri Lanka's opposition has also objected to the election and is considering supporting a common opposition candidate.
One of the main demands of the opposition is for the executive powers in the hands of the president to be abolished through constitutional reforms. But Rambukwella said only parliament has the powers to consider such a demand.
He said a Parliament Select Committee (PSC) which had been appointed to look at such proposals has been unable to move forward as the opposition has boycotted the committee meetings.
"There needs to be inclusive participation by the opposition in the (PSC) and only the PSC can propose constitutional changes. The government cannot on its own make such changes," he said.