The Prime Minister received Sen at his official Temple Trees residence for the talks, officials said.
Details of the talks were not disclosed, but Rajapakse had said on Wednesday that he was seeking support from the other three Test playing nations in South Asia -- Bangladesh, India and Pakistan -- over the issue.
Rajapakse is also making elaborate arrangements to welcome Muralitharan on his return later in the day after Sri Lanka's tour of Zimbabwe where he broke the world record for most number of Test wickets.
The Sri Lankan Prime Minister mounted a campaign to defend the star off-spinner after he was reported for suspect bowling action by ICC match referee Chris Broad during the home series against Australia last month.
Rajapakse snubbed ICC president Ehsan Mani's who adviced politicians to stay out of the Muralitharan row and allow the ICC to deal with the situation.
Australian Prime Minister John Howard added spice to the debate on illegal bowling action last week when he said Muralitharan was a chucker, prompting the world record-smashing spinner to consider boycotting Sri Lanka's tour of Australia in July.
Rajapakse said Muralitharan, the most successful bowler in Test history, was a national asset and he would do everything within his power and that of the Government to defend the bowler.