"I think it is the wrong decision not to tour," Warne was quoted as saying by Melbourne's Herald Sun newspaper.
"He should keep doing what he loves doing and that's playing cricket. He has a lot of critics, particularly in Australia, but you can't afford to let the critics get to you."
The Australian leg spinner said Muralitharan's decision was "thin-skinned" and added that he hoped the Sri Lankan had not been influenced by his controversial former captain, Arjuna Ranatunga, the newspaper said.
"Hopefully, he has not been listening too much to Arjuna, but he's always stirring the pot," said Warne.
"I was looking forward to going head to head with Murali again. I'm really disappointed that he has decided not to come to Australia.
"It's disappointing for everyone, the players and the public. I suppose he will not tour a lot of countries now.
GREAT CHALLENGE
"Our players batted very well against him in Sri Lanka (winning the series 3-0 in March), and it would have been a great challenge for him to see how he went in Australia."
Warne trails Muralitharan's world record of 527 wickets by only 10 victims.
However, the 34-year-old Warne broke his hand while batting for his English county side Hampshire last week and is doubtful for next month's two-Test series against Sri Lanka in Darwin and Cairns.
Sri Lanka's controversial and unorthodox off spinner had been considering whether to pull out of the series after fresh doubts over his bowling culminated in Australian Prime Minister John Howard calling him a "chucker".
Muralitharan was called for throwing on two previous visits to Australia.
The Sri Lankan national hero was reported to the International Cricket Council by match referee Chris Broad during the home series against Australia in March.
Broad was concerned about his 'doosra', a leg break variation.
Biomechanical tests at the University of Western Australia showed the 32-year-old's arm straightened during delivery and he was told to stop bowling it.
Previous tests on his normal action, however, have backed Sri Lankan claims that it is legal. The issue is further confused since the bowler cannot fully straighten his arm due to a birth defect.
