National's support partners, the Maori Party and Act, say their ongoing support for the legislation is not guaranteed.
Prime Minister John Key said this afternoon he was not taking other parties' support for granted.
"Anything is always possible ... but I suspect there is overwhelming support for what is a really important step from an environmental perspective."
Maori Party leader Marama Fox said iwi recognised the importance of setting aside areas for conservation.
But the Government needed to ensure that it recognised Treaty settlements in full, she said, noting that just two of 58 iwi with interests in the Kermadecs had been consulted on the sanctuary.
"Nobody disputes the idea that a sanctuary of this nature isn't a fabulous opportunity. The issue is that the Government should have consulted with iwi."
Act Party leader David Seymour said he would pull his support unless the Government compensated the affected fisheries.
He said the sanctuary was a "PR exercise" because it mostly contained migratory species which could be caught elsewhere.
National will still have the support of its support partner United Future, as well as the Labour Party.
The Green Party has also indicated it will support the law change -- the first time it has backed a Government bill on environmental protection since mid-2014.
Green Party environment spokeswoman Eugenie Sage said fisheries legislation clearly stated that the Government could introduce marine reserves without needing to pay compensation.
"I don't see the [legal challenge] as an obstacle to the bill proceeding," she said.
