Rajapakse said in a statement on Sunday that he would defend the off-spinner even though Sri Lanka Cricket had asked the bowler to cut out the away-going delivery from his armoury.
"The Prime Minister has decided to take legal steps against the ICC for banning (Muralitharan's) doosra," a statement from his office said. "The Prime Minister is already in consultation with a team of lawyers."
Rajapakse said that Muralitharan, who is now the most successful bowler in Test history with 523 wickets, was a national asset and he would do everything within his power and that of the government to defend the bowler.
Muralitharan, whose unorthodox action has seen him being no-balled for 'throwing' in the past, came under fresh scrutiny because of the 'doosra' and was told last week that if he persists with it he could face an year-long ban.
The off-spinner was sent to Australia to work on his action with a biomechanical expert after he was reported by a match referee last month.
After the first stage of the review process had been completed, ICC chief executive Malcolm Speed said the report forwarded to him by Sri Lanka Cricket (SLC) but compiled by the University of Western Australia, meant the 'doosra' could no longer be tolerated.
"The report forwarded by Sri Lanka Cricket proves that the degree of straightening is well outside the ICC's specified levels of tolerance," said Speed.
"In light of this finding, Sri Lanka Cricket has now informed the ICC that it has instructed Mr Muralitharan not to bowl this delivery in international cricket. The ICC supports this action," he added.
The report showed an initial straightening of the arm of around 14 degrees which after some remedial work was reduced to 10 degrees, five more than the level of tolerance for spinners.