The Scottish government has said that it will withhold legislative consent on the Conservative proposals to scrap the 1998 Human Rights Act, as it emerged that the SNP has already had informal discussions with Tory backbenchers who oppose the move.

The social justice secretary, Alex Neil, told the Holyrood chamber on Tuesday afternoon: “The Scottish government’s position is that implementation of the Conservative government’s proposals would require legislative consent and that this parliament should make clear that such consent will not be given.”

Tory plans to repeal the act and replace it with a UK bill of rights could lead to a “complete standoff” between Westminster and Holyrood, according to a Scottish government source.

A senior SNP source confirmed that the party had been in contact with potential Conservative backbench with a view to bolstering cross-party opposition to the move.

The Guardian understands that the Scottish government may seek legal advice as it wrestles with the potential implications of the proposals.

Neil told the chamber: “There is currently insufficient detail in what is proposed to predict the impact on Scotland with any certainty. However, given the almost unanimous opposition in this parliament and among Scottish MPs at Westminster, it would remain open to exclude Scotland from legislation to repeal the Human Rights Act or for the Scottish government to pass legislation to give effect to a range of rights in policy areas which are within devolved competence.”

Under devolution legislation, acts of the Scottish parliament and decisions of Scottish ministers must comply with the European convention and the 1998 Human Rights Act. To further complicate matters, although the act is reserved, human rights issues are devolved. This creates two different human rights regimes across the UK which could technically act as a lock on Westminster moves.

In practice, the Scottish parliament would be invited to refuse legislative consent via a Sewel motion. The Sewel convention applies when the Westminster parliament legislates on a matter which is normally dealt with by the Scottish parliament and can happen only if Holyrood has given its consent

However, in an interview on BBC Radio Scotland’s Good Morning Scotland programme on Tuesday, the new Scottish secretary and Scotland’s only Conservative MP, David Mundell, insisted that there would be no conflict. He said: “New legislation replaces existing legislation and therefore the new act will apply in Scotland.

The minister said his “door was open” to discussions on any issue with the Scottish government, but that those talks should not happen “through the media or public posturing”. He added: “I think people in Scotland share the concerns that have been voiced across the UK that we have got the balance wrong between rights and responsibilities.”

It is understood that the question was raised at Tuesday afternoon’s first parliamentary group meeting of the expanded cohort of new SNP MPs. Following a meeting of the Scottish cabinet on Tuesday morning, the first minister, Nicola Sturgeon, will be writing to Cameron to request a meeting in the near future to discuss this and other issues arising from the election of the new Conservative government.

Further evidence of the immediate and growing opposition faced by the Conservative party to its flagship proposal came as concerns were raised in Northern Ireland that scrapping the act could amount to a breach of the Good Friday agreement. Wales similarly has a different arrangement under devolution.

The Ukip MEP Diane James described the Conservative plan as a fraud on Tuesday. She said: “Article 7 (TEU) of the Lisbon treaty gives the European council the power to strip a member state of its EU voting rights if it decides the state is in breach of Brussels’ definition of human rights. This is EU law. And since EU law is at all times superior to UK law, as long as we are members of the EU our supreme court will be supreme in name only.”