''We shouldn't be dancing to the Greens' tune,'' Dr Emerson said.
But several MPs took exception to Dr Emerson's comments, which they saw as an attempt to ban attendance at the meeting.
''I told him I'd be going anyway,'' New South Wales backbencher Laurie Ferguson later told The Age.
''What he doesn't appreciate is there is no contradiction between the Labor Party platform which says that we respect the integrity of Indonesia's boundaries … and a campaign for human rights in West Papua and for support for discussions on autonomy,'' he said, adding that parliamentary groups met on similar issues such as Palestine, Western Sahara and Tibet.
Dr Emerson was also pulled up by Labor caucus chairman Daryl Melham and former Speaker Harry Jenkins, who said MPs were free to attend any event they chose.
Labor backbenchers Melissa Parke and Claire Moore also attended the meeting.
West Papua was incorporated into Indonesia in the late 1960s but has been beset by a long-running campaign for independence.
The Indonesian embassy yesterday declined to comment.
But Northern Territory Labor senator Trish Crossin, who chairs the Australian Indonesian Parliamentary Friendship Group, confirmed a delegation of embassy officials had met her yesterday to express concern because West Papua is a province of Indonesia.
Senator Crossin spoke in support of Dr Emerson in caucus and said it was unclear what the meeting was meant to achieve as friendship groups are usually country to country.
''If it's an informal little group to advocate for human rights there - well, that's totally separate.''