Pete Wishart joined SNP colleague Angus Brendan MacNeil in abstaining on one of the proposals in Wednesday night’s indicative Brexit votes, against the party whip.
“This confirmatory vote also has serious consequences for our future independence referendum,” Mr Wishart said in a blog post.
“In supporting this we might be expected to support a ‘confirmatory’ referendum for any deal we negotiate with the UK to secure our independence.
“This would be an open invitation for those opposed to our nation’s independence to try and undermine that result.”
The SNP’s 35 MPs were also criticised for abstaining on a call for any Brexit deal to include a customs union with the European Union, a proposal that fell by just six votes on Wednesday night.
Labour MP Ian Murray accused the Nationalists of “game playing”.
He said: “It’s clear that the SNP cares more about constitutional chaos, indyref2 and grievance than finding a solution to Brexit, in the desperate hope of boosting support for the break-up of the UK.”