Attorney-General Chris Finlayson will take over the Labour portfolio in an acting role, but Ms Wilkinson will keep her conservation portfolio and remain in Cabinet.
Asked why she did not resign from Cabinet, Ms Wilkinson said: "I've done nothing wrong."
The Royal Commission report released yesterday said the Department of Labour had failed to maintain health and safety standards in the mining industry.
Labour Leader David Shearer would not call for Mr Key to strip Ms Wilkinson of her other portfolios, however he said the Prime Minister should "take a good look" at what she was doing in them.
"Given the fact that in this case she advised us when we wrote to her that there was no problem with health and safety in mines, they should be looking very closely what she's doing in her other portfolios."
Mr Shearer said Labour's MPs would "search" themselves as to whether they could have done more while in Government to prevent the disaster, but the party had tightened up relevant legislation in 2003 and Trevor Mallard while Labour Minister in 2008 initiated a review of mine safety.
That review produced a set of recommendations "which the National Government did not take up" he said.
Mr Mallard said that review made clear the need for "check inspectors" or mine workers with an official safety oversight role.
"We were on track to change the Mining Act as a result of that review. The review was scrapped by Kate Wilkinson, and that's something I think is very regrettable.''
Mr Mallard said he had thought about the mine safety issue "every day since Pike River".
"People died. I ask myself is there more I could have done? But I'm absolutely certain that we were on track. We had a review process, it was working well. It was being resisted by mine owners, but my view is that the regulatory environment would have changed."
