Scottish Government independence minister Jamie Hepburn has said he would "never seek to influence" the civil service after Rishi Sunak backed a probe into spending on independence.
The SNP-Green administration has published the first five of a series of position papers setting out its case for constitutional change in Scotland, with a team of officials supporting Hepburn.
The matter has provoked criticism from figures including Scottish secretary Alister Jack and Labour peer George Foulkes.
On a visit to Scotland on Monday, the prime minister said he supported an investigation by cabinet secretary Simon Case, head of the UK civil service, into Scottish Government spending on independence.
John-Paul Marks, Scotland's most senior civil servant, has defended the role of officials in supporting the Scottish Government to build its case for a Yes vote.
However, Case told members of the House of Lords it would be "worrying" if public money is being used to support ministers who want to break up the UK. In an exchange with Foulkes, he said an investigation into the matter is taking place and new guidance could be issued within weeks.
Speaking in Aberdeenshire on Monday, Sunak backed Case's work, saying it is "right" to "let that continue" and Scottish people do not want to see "more constitutional wrangling".
His comments came after Jack wrote to first minister Humza Yousaf stating that "to use Scottish Government funds and civil service resources to design a prospectus for independence or support a minister is simply irresponsible".
Now Hepburn has told CSW sister publication Holyrood that he would "never seek to influence" Marks.
He said: "I would never seek to influence him in any way, shape or form. The operational independence of the civil service is important."
He added: "There's a certain irony in unelected members of the House of Lords saying the Scottish Government can't undertake certain forms of activity when they have no elected mandate, unlike the Scottish Government."
The Scottish Government's Building A New Scotland series was launched by Nicola Sturgeon before she left office. She promised the publication of 10 papers, but said the administration would "not be limited" to that number.
Five have been published so far, two of which – on a written constitution and citizenship criteria – have been released under Yousaf's leadership.
Asked in Aberdeenshire if he was concerned about the Scottish Government's spending on the series, Sunak said: "What's right is that, as the head of the civil service, it's Simon Case who conducts a review of that particular situation and I think it's right that we let that continue."
He said reducing inflation, easing the cost-of-living crisis, growing the economy and cutting waiting lists are "what people would want to see in Scotland", stating: "I've always said I'm always happy to work constructively with the Scottish Government to deliver for people in Scotland."
This story was written by Kirsteen Paterson, who writes for CSW's sister publication Holyrood, where this story first appeared