The Abbott government has imperilled its future relationship with key crossbench senator John Madigan - whose vote it may need to pass legislation - by its handling of the West Papua protest in Bali.

The Democratic Labour Party senator, a supporter of West Papuan rights, was furious over a story on News Ltd websites on Monday claiming he had warned Prime Minister Tony Abbott of a planned Papuan protest at Australia's consulate in Bali.

He believed the Prime Minister's office was the source of the story and that its intention was to discredit him by making him appear too closely involved with the West Papuan rights movement.

''The ALP never pulled a stunt like this in the two years and three months I've been in the Senate,'' he said. ''I tell you, they're not off to a good start with me.''

Asked whether it would tarnish his future dealings with the Abbott government, he said: ''Well it doesn't bode well, does it? How would you feel?

''From now on, anything they say to me is going to be viewed with highest suspicion. Nothing will be taken at face value.''

Senator Madigan's vote could be crucial for the Abbott government to pass key legislation through the Senate including scrapping the carbon and mining taxes.

Senator Madigan was also angry at the government's handling of an incident in which three Papuan men scaled the wall of the Australian consulate in Bali early Sunday morning to demand Australia back greater political freedoms.

He said that he called Mr Abbott only after the news had broken about the three men entering the consulate grounds, once at 7.54am Melbourne/Sydney time and again at 10.20am.

Mr Abbott called him back at 2.34pm and left a message for Senator Madigan saying the Australian government did not support such ''grandstanding'' over the West Papua issue and that Australia absolutely supported Indonesian sovereignty over the province.

Mr Abbott's spokesman did not dispute the time of those calls but declined to comment further.