Howard entered the fray on Friday when he said he believed Muralitharan was a chucker, prompting Test cricket's world record wicket-taker to consider boycotting his country's tour of Australia in July.
Rajapakse has also upset the International Cricket Council (ICC) by announcing his intention to sue the ICC over its decision to outlaw the spinner's "doosra" delivery, which recent Australian scientific analysis showed was illegal.
Mani has defended his organisation's handling of Muralitharan's suspect bowling action, saying Howard and Rajapakse should stay out of the debate and allow the ICC to deal with the situation.
"The Murali issue has sort of blown out of proportion because of various remarks by various politicians," Mani was reported in Sydney as saying from London.
"I've heard various versions of these comments, but obviously it's not helpful when high-profile people make these sort of comments.
"I wish they'd talk to us first rather than making statements in the public arena."
In a statement, Rajapakse said Muralitharan was "a national asset" and he would do everything in his and the Government's power to defend the bowler.
But Mani said he had no concerns over the ICC's banning of Muralitharan's doosra.
"I don't know the basis of how we'd be sued, but all our regulations are fully supported by all our members," said Mani, referring to the fact the Sri Lanka Cricket (SLC) is part of the ICC.
Muralitharan's suspect action will be put under further scrutiny at the Champions Trophy tournament in England in September.
As well as experimenting with umpires having earpieces linked to stump microphones at the tournament, the ICC has announced it would conduct research into spin bowling and spinners' actions.
All spinners taking part in the tournament will be scrutinised by high-speed cameras behind the bowler's arm and square of the wicket.
Footage from the cameras, which capture images at 250 frames per second, will be fed into a software package to break down spin bowlers' actions.
But the ICC said the spin bowling scrutiny was not aimed at Murali.
"The research is not targeted at any individual or any individual's action," ICC general manager David Richardson said. "It will be across the board."