But several MPs including Laurie Ferguson of NSW, Fremantle's Melissa Parke and Claire Moore, Labor senator for Queensland, said that they planned to attend a meeting of the group anyway.
A fired-up Mr Ferguson told The Australian later he did not think Mr Emerson was across the portfolio when he came up with "this preposterous idea".
He said the minister's intervention was ridiculous and unprecedented. For decades Australian MPs of every persuasion had been free to support a very wide range of causes.
"In no way is the group about destroying the integrity of Indonesia's boundaries," Mr Ferguson said. "But that doesn't mean there should not be a discussion about a degree of autonomy for West Papua as there is in Aceh."
Mr Ferguson said that through the day other Labor MPs had declared their support for the West Papuans.
Mr Ferguson said those involved were concerned about human rights abuses in the province and the very heavy military presence there. "People have been jailed for 15 years for putting a flag up," Mr Ferguson said.
The Greens' spokesman for West Papua, Richard Di Natale, said it was disappointing that there should be division "over protecting the fundamental human rights of our neighbours in West Papua".
"Craig Emerson's stance on this issue is cowardly," he said. "I'm pleased that a number of Labor Party members took a stand."
Orginal news: Theaustralian.com.au/news