The Perth and North Perthshire MP has voiced concerns that the SNP's position could undermine a future Yes vote on Scottish independence referendum by opening the door to a second vote on that issue.
But Mr Wishart, who chairs the Commons' Scottish Affairs committee, has warned that a second vote would set a problematic "precedent" for the Yes campaign in a future referendum campaign, in an article for today's National.
“By enthusiastically buying into this ‘confirmatory’ vote for an EU referendum we weaken our hand in resisting unionist calls for a second vote on a successful indyref," he writes.
"You can just imagine the unionist chorus – ‘you were all for a second confirmatory vote on the EU but not one for independence’?”
“And if they were successful in using this precedent against us, unreconciled unionists would be working non-stop from the day after the referendum to ensure that a successful outcome would be overturned. Every apparatus of state would be deployed and they would ensure that the worst possible ‘deal’ would be offered to the Scottish people in the hope that their union could be rescued.”
"When it comes to a People's Vote, the SNP's heart has never been in it," he said.
"Everything is seen through the prism of independence for the Nationalists, putting party interest ahead of the country's interest.
"This is typical of the SNP - it's independence at all and any cost.
"We are inching towards a parliamentary majority for a People's Vote, so this raises questions about how Pete Wishart and other SNP MPs will vote in the Commons.
"Nicola Sturgeon repeatedly failed to back a People's Vote, then added the condition of a second independence referendum, and now only backs it with that condition silently in the background. She must urgently distance herself from Pete Wishart's comments and wholeheartedly back a People's Vote."