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First Minister John Swinney says that relations with the UK government have "haemorrhaged" with Douglas Alexander as Secretary of State for Scotland.
Prime Minister Andy Burnham announced on Monday that Alexander would remain in his role. Alexander said he was "very happy" to keep the job.
But Swinney has raised concerns over Burnham's decision and accused Alexander of "making life difficult" for Scotland.
Alexander began the role in September 2025 after the sacking of Scottish Labour's longest serving MP, Ian Murray, in a UK government reshuffle.
Swinney told BBC Radio Scotland Breakfast: "We enjoyed a pretty constructive relationship when Keir Starmer appointed Ian Murray as Scottish Secretary.
"But I have to say that pretty much haemorrhaged with Douglas Alexander's arrival.
"The prime minister assured me yesterday that he is interested in a collaborative relationship.
"I take that at face value and I hope that is reflected in the approach that is taken by the Secretary of State for Scotland."
Swinney said there had previously been "excellent cooperation" between the Scottish government and the Scotland office led by Murray.
But Alexander's arrival coincided with his appointment as joint director of the Scottish Labour Holyrood election campaign to get Swinney out of office.
Swinney said at this point "relations soured significantly".
The first minister added he had known Alexander for decades since the pair were students at the University of Edinburgh.
"I bear nobody any personal ill will, I'm not interested in that," Swinney said.
"I am interested in improving the lives of people in Scotland.
"If I have to battle past a Secretary of State for Scotland that is making life difficult, then it just makes it even more difficult for me."
The Scotland Office has been approached for comment.
Swinney also told the BBC Radio Scotland that he does not agree with Andy Burnham's views on regional mayors.
Burnham said one of his key priorities for Britain would be to hand more power to councils and authorities away from Westminster.
The former mayor of Greater Manchester vowed to give mayors greater control over social housing, welfare and education.
Swinney said that while he plans to strengthen local council powers in Scotland, he does not support "the concept of mayors".
"I believe in the democratic tradition of electing local authorities and for those authorities to be accountable to the people that elect them," he added.
Burnham stood down as an MP to be elected as the first mayor of Greater Manchester in 2017 in a time when regional mayors where an untested concept.
Democratic accountability
Swinney added that the Scottish government was supporting councils, city region deals and ensured that local authorities had more say over finances.
He said: "A lot of good things have happened in Manchester but there are a lot of good things that have happened in the Glasgow City deal or the Tay City deal or South East of Scotland deal.
"These are where local authorities have worked together with the Scottish government and the UK government in a collaborative programme of delivering projects and nobody's democratic accountability has been undermined as a consequence."
Burnham and Swinney spoke on the phone on Tuesday morning for the first time since the prime minister took office.
The Scottish government spokesperson said Swinney also used the call to extend an invitation to the PM to visit Scotland.
