Muralitharan on Saturday said Howard, a keen cricket fan, should concentrate on running Australia rather than passing judgement on his controversial bowling action.
Muralitharan, the top Test wicket-taker of all time with 523 wickets, said he was considering sitting out of a tour to Australia in July because of Howard's remarks.
"Definitely, because the Prime Minister of Australia shouldn't be saying things like that," Muralitharan told Australian Associated Press from Bulawayo after day one of the second Test against Zimbabwe.
"The Prime Minister shouldn't be saying things like that, he doesn't know the facts."
Muralitharan said he would speak to the Sri Lankan Government about whether to tour because Howard's remarks had made the matter a political issue.
"You can't accuse people of being a chucker," he said.
"It's out of line because he shouldn't be saying those things, he should be thinking of his country. It's not good enough."
Muralitharan said last year that he was considering avoiding Sri Lanka's two Test matches against Australia in Darwin and Cairns because of constant taunting by Australian crowds since he was no-balled for throwing there in 1995-96.
Muralitharan has a genetic defect which stops him fully straightening his bowling arm upon delivery.
He was reported for a suspect action by English match referee Chris Broad during the third and final Test of the March series in Sri Lanka which was won 3-0 by Australia.
Perth-based biomechanics experts subsequently tested him and initially found he straightened his bent arm by 14 percent in bowling a delivery tagged the "doosra".
The doosra is a delivery which spins away from right-handers instead of coming into them like a normal off-break.
Under remedial work, Muralitharan reduced the arm straightening to 10 percent, which is still twice the amount allowable for spinners under International Cricket Council (ICC) regulations governing illegal bowling actions.
After being reported to the ICC, Muralitharan has been ordered to stop bowling his doosra or face being suspended for up to a year.
Asked by a party faithful in regional New South Wales state on Friday if he thought Muralitharan was a chucker, Howard replied: "Yes."
"They proved it in Perth too, with that thing," He added, drawing an image of a video screen with his hands.
Muralitharan's delivery has faced intense scrutiny in Australia because he pipped controversial local hero Shane Warne in breaking West Indian Courtney Walsh's record of 519 Test wickets.