Scotland cannot be taken out of the European Convention of Human Rights (ECHR) without Holyrood's consent, Ruth Davidson has said.
Davidson criticised the UK Home Secretary Theresa May for her stance in favour of leaving the ECHR regardless of the outcome of the EU referendum.
May has said she wants to see Britain leave the ECHR to make it easier to deport potentially dangerous foreign nationals.
The Home Secretary said in April: "Regardless of the EU referendum, my view is this: if we want to reform human rights laws in this country, it isn't the EU we should leave, but the ECHR and the jurisdiction of its court."
The Scottish Conservative leader claimed the situation was "a little bit more complicated" than May had suggested.
Davidson also said the UK had played a large role in drafting European human rights law, adding that the ECHR is enshrined with "British values".
Speaking in an interview with LGBT news website PinkNews, Davidson said: "I think it's a little bit more complicated than Theresa May is trying to push out there."
"I take a slightly different view from Theresa May - I think we should recognise that the ECHR was in large part drafted by people from Britain, and it's British values that are enshrined there."
The Tory leader added: "In terms of a Scottish context, the ECHR is written into the original Scotland Act, so it would be up to the Scottish Parliament to decide whether we changed the basis of that.
"There's nothing at a UK-wide level that would be able to change that without Holyrood's consent."
Davidson was happy to defend the UK government's "draconian cuts to disability benefits", the SNP said.
A party spokesperson said: "While Ruth Davidson has, rightly, spoken out against Theresa May's call for the UK to leave the ECHR, she wasn't so quick to criticise the UK Government for their attempts to make draconian cuts to disability benefits earlier this year.
"If Ruth Davidson is serious about defending human rights she will join every other party leader in the Scottish Parliament in opposing the UK government's wrong-headed plan to repeal the Human Rights Act.
The SNP added: "Theresa May's comments are a reminder that we need an SNP Scottish Government with the strength to stand up to a deeply regressive Tory government - and the only way to ensure a re-elected SNP government with Nicola Sturgeon as First Minister is to cast both votes for the SNP."
The Scottish Lib Dems said Davidson was part of the "David Cameron and Theresa May fan club".
Party leader Willie Rennie said: "The Home Secretary is wrong on the ECHR but this says more about the hopeless splits in the Conservative Party on Europe than Ruth Davidson's commitment to human rights.
"Ruth Davidson is backing David Cameron and Theresa May on the illiberal snooper's charter. She backed George Osborne on his cuts to benefits that would have taken thousands of pounds from disabled people.
"Everyone knows that Ruth Davidson is a fully paid up member of the David Cameron and Theresa May fan club every day of the week. This artificial distance won't fool anyone."
The Greens said the Scottish Tories were "desperate" to distance themselves from their UK counterparts.
Justice spokesperson John Finnie said: "Another day, another desperate attempt by Ruth Davidson to distance herself from the toxic Tories she represents.
"In 2014 Tory MSPs including Ruth Davidson voted against a motion supporting the European Convention on Human Rights, so the 'slightly different' view from Theresa May she now claims cuts no ice."
Finnie added: "The Tory Government's proposed Bill of Rights is legally illiterate. It's one of many reasons we need a bolder Holyrood with more Green voices, so Scotland stands firms against a right wing assault on human rights."
We can opt in or out of the ECHR whether we stay in the EU or not, the Leave campaign in Scotland said.
The director of Scottish Vote Leave Tom Harris said: "This Tory squabble highlights the fact that the EU doesn't protect our rights - whatever the Remain camp claim, we can opt in or out of the ECHR regardless of whether we're in the EU."
The Remain campaign said only staying in both the ECHR and the EU would "protect our human rights across the board".
A spokesperson for Scotland Stronger In Europe: "Remaining in the European Union is vital to protect our human rights across the board.
"That includes ECHR, but also important workers' rights enshrined in European law - including health and safety standards at work, equal treatment for men and women, maternity and paternity leave, maximum working hours, and paid holidays.
"These are all significant advances achieved at European level, and the way to protect these gains is to vote Remain on 23 June."
A source also said the Leave campaign were wrong to say a country can opt out of the ECHR while staying in the EU. Signing up to the ECHR is part of the accession criteria to EU membership, the source said.
Scottish Labour have been approached for comment.