Labour peer Lord Foulkes said the “deliberately provocative” publication should be halted.
Humza Yousaf and his independence minister Jamie Hepburn are due to issue the fifth paper in their Building a New Scotland series, which focuses on citizenship, on Thursday.
It will set out who could become a Scottish citizen automatically following a vote for independence, and the pathway for others to qualify.
The paper will also include migrant rights, freedom of movement, proposals for Scottish passports, and a network of diplomatic staff overseas.
Publication is set to heighten a growing cross-border row about civil servants in Scotland working on independence despite constitutional issues being reserved to Westminster.
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The Scottish Tories said it was an “utterly unaceptable” use of resources.
Last week, the head of the UK civil service, the Cabinet Secretary Simon Case, told peers it would be “unusual and worrying” for officials to work on breaking up the UK.
He told the House of Lords’ Constitution Committee that new guidance would be issued to civil servants “within weeks” on the issue.
Scottish Government spending on Mr Hepburn’s remit is also being investigated by the advocate general for Scotland, Lord Stewart, the UK Government’s top adviser on Scots law.
Around 20 officials are reported to be working on the Building a New Scotland series, with salary costs for the Constitutional Futures Division around £1.4million in 2022/23.
SNP Westminster leader Stephen Flynn last night wrote to Mr Case complaining about the UK Government exerting “ever tighter controls of Scotland’s national democratic institutions”.
Mr Hepburn said: “As an independent nation, Scotland would have the opportunity to re-define what it means to be a citizen of this country, building on our inclusive national identity and sense of collective purpose.
“Independence would also enable us to take a fairer and more welcoming approach to citizenship to make it easier for those who have made Scotland their home to settle here permanently, helping to grow our population and support our communities and public services.
“The proposals in this paper explain how we plan to achieve these aims, on the way to re-joining the European Union as an independent nation, and I look forward to setting them out with the First Minister on Thursday.”
The SNP-Green government, which commands a majority of MSPs at Holyrood, says it has a mandate from voters at the 2021 election to work on furthering independence.
However that has been queried at Westminster since Nicola Sturgeon’s had the question of Holyrood holding a unilateral referendum referred to the UK Supreme Court.
The Court ruled unanimously that Holyrood did not have the power to hold a referendum without Westminster’s consent, raising questions about Scottish ministers continuing to order their officials to work on a policy they knew they could not deliver in practice.
Scotland’s top civil servant, the Permanent Secretary John-Paul Marks, recently defended the status quo, saying officials “serve the Scottish Government and their priorities”.
However at the Lords committee last week, Labour peer George Foulkes asked Mr Case: “If civil servants are effectively supporting ministers who want to break up the United Kingdom, and these are United Kingdom civil servants paid for by taxpayers’ money, it would be a bit unusual and a bit worrying, wouldn’t it?”
Mr Case replied: “I agree with you. I think it would be unusual and a bit worrying. Which is why we are looking at the specifics of cases that you and other members raise regularly in correspondence.”
Stressing the need to ensure the civil service remained impartial, he added: “To be clear, I believe that they have been looking at these edge cases diligently.
“But as I say, I want to go back round them all with colleagues in Scotland and with ministers to make sure we are doing absolutely what we should to protect and preserve that impartiality.”
Asked when the guidance would be published, Mr Case said: “I hope it will be weeks.”
Mr Flynn said Westminster was seeking to “stop the Scottish Government from carrying out the work it was elected to do” .
He said he had “no argument” with Whitehall supporting the UK Government’s policy of supporting the Union, but struggled to see why such work would be deemed “impartial” while Scottish Government work on independence would not.
Demanding a “clarification” on the matter, he told the Cabinet Secretary he felt “alarm” at his comments to the Lords committee.
Scotland was “a nation, not an administrative unit subservient to Westminster”, he said.
The Aberdeen South MP said: “The Scottish Government also elected on an explicit commitment to provide the people of Scotland with the information they need to make an informed decision over their future.
“The fact that attempts are now being made not only to deny people in Scotland the right to decide their own future, but to stop the Scottish Government from carrying out the work it was elected to do, will reinforce the sense that Westminster is not interested in working in partnership but is only concerned with exerting ever tighter control on Scotland’s national democratic institutions.”
He said the UK Government was “clearly active in attempts to counter pro-independence arguments” and previously set-up a “Union Hub” under Michael Gove to promote the Union.
The Prime Minister also chaired a “Union Strategy Committee” and the Scotland Office’s budget had increased as it took an “increasingly assertive… anti-independence stance”.
He asked Mr Case if he agreed with one of his predecessors, Sir Gue O’Donnell, who said Scottish ministers were “elected on the basis of a stated manifesto commitment that there should be a referendum on independence” and it was therefore “entirely consistent with the principles of the Civil Service Code that civil servants should support their Ministers in the development of that policy”.
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Lord Foulkes told the Herald: “It would be outrageous if they go ahead.
“We now know that Simon Case agrees it is of concern if civil servants are being deployed by Scottish Government on these subjects and is investigating.
“This would be deliberately provocative and they should think again.”
Tory MSP Alexander Stewart said: “These independence plans are blatant misuse of public money and resources by the SNP – civil servants are supposed to support the government’s agenda, not push the Nationalists’ pet project at taxpayers’ expense.
“The SNP are constantly blurring the lines between party and government.
“It is utterly unacceptable for the SNP to be wasting taxpayers’ money and civil servants’ time on pushing a divisive party political agenda which the Scottish government lacks the authority to pursue unilaterally.
“This is the wrong priority at the worst time, when Humza Yousaf and his ministers should be concentrating on unacceptable NHS waiting times and the cost of living crisis. Only the Scottish Conservatives are focused on Scotland’s real priorities.
“The SNP must drop their independence obsession and instead devote every penny towards helping our struggling public services.”