David Cameron's Government has been accused of treating Scottish MPs as "second class" just weeks after the independence referendum.
Labour MPs have protested after what they say was an attempt to undermine their authority by the back door.
The row erupted after a Cabinet minister appeared to suggest she did not have to answer a question in the Commons because it came from a Scottish MP.
The MP in question, Glasgow North West's John Robertson, has made a formal complaint to the Speaker of the Commons, John Bercow.
The controversy comes amid fears over the potential effect of Mr Cameron's planned move to restrict Scottish MPs' voting rights.
Labour have accused the Tories of attempted gerrymandering with their push for "English votes for English laws". Scottish MPs say that even the Conservatives' plans would not bar them from asking ministers questions.
The row was triggered when Mr Robertson asked Nicky Morgan, the Conservative Education Secretary, about the Coalition Government's policy to allow unqualified teachers to work in some English schools.
Ms Morgan, who is also the Coalition's equalities minister, pointed out that the issue under discussion did not affect constituents north of the Border.
She said: "I do note as a Scottish Member of Parliament you are asking about English educational standards but I'm very happy to answer your question."
In his letter to the Speaker, Mr Robertson wrote: "I am concerned that even before any legislation regarding English devolution has been passed by the House, Scottish MPs as well as those from Wales and Northern Ireland are treated as second-class.
"I would like to ask your advice on whether this behaviour should be tolerated by the chair.
"This is a pertinent question as it would also bring into question whether the many English MPs who ask questions in Scotland, Wales and Northern Ireland departmental questions should be allowed to do so."
Mr Robertson said: "In the Commons, all MPs are able to ask questions to all departments. This should be welcomed, because we gain from having different views debated."
He added: "Instead of listening to the Scottish people, the Tories have instantly used the result to play their own political games.
"They should be focusing on delivering on their promises, rather than limiting themselves to starting a whole new debate on English devolution."
The row came just days after the Prime Minister repeatedly asked Ed Miliband about the NHS in Wales, an issue which MPs say does not affect Mr Cameron's constituents in Oxfordshire.
Ms Morgan's office declined to comment. A spokesman for Mr Bercow said he did not comment on private correspondence between the Speaker and MPs.
Mr Cameron was accused of betrayal after he announced plans for "English votes for English laws" within hours of the independence referendum result.
The move also drew ire from constitutional experts.
Vernon Bogdanor, professor of government at King's College, London, who taught both David Cameron and Nick Clegg, has warned the idea is incompatible with the Union. "The British model of government requires a government that is collectively responsible for all matters, not just a selection of them," he said.
The Tories insist the present system is unfair because it allows Scottish MPs to vote on a number of issues, including health and education in England, that do not affect their constituents.
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