Humza Yousaf has dismissed claims he is wasting taxpayers’ money on independence campaigning.
Scottish Secretary Alister Jack sent a letter to the first minister saying the government was putting its “obsession with independence ahead of pressing priorities in Scotland”.
Mr Yousaf launched the latest in a series of papers setting out the case for independence this week.
He said the SNP were elected on a mandate to deliver a referendum.
Speaking to BBC Scotland, Mr Yousaf added he felt “comfortable” using public funds to promote independence.
The first minister launched a new Scottish government paper on Thursday that set out plans for citizenship and passports in an independent Scotland.
It is the fifth in the Building a New Scotland series, which was launched by former first minister Nicola Sturgeon last year.
Opposition MSPs have labelled the plans a waste of taxpayers’ money.
In response to the publication, Mr Jack wrote to Mr Yousaf saying it was his “strong view” that ministers had “a responsibility to spend taxpayers money wisely.”
He said: “It therefore seems clear to me that to use Scottish government funds and civil service resources to design a prospectus for independence or support a minister for independence is simply irresponsible.”
Mr Jack added that it was “particularly true” given that the Supreme Court has ruled the Scottish government cannot hold a referendum without UK government consent.
Speaking in Rutherglen, Mr Yousaf rejected the criticism, saying he was “not surprised” the Scottish secretary wanted to stop advancing a positive case for independence.
He said: “What I would say to Alister Jack and others, is instead of trying to shut down the debate, respect democracy here in Scotland.
“Give us that second independence referendum and let’s have that debate in a full, frank, transparent manner instead of trying to do the undemocratic thing and shut it down.”
The first minister added that the SNP was elected on a manifesto that promised a second independence referendum.
He said: “It’s really important it’s an informed debate so we’re doing, of course, the responsible thing by presenting the positive case, giving people the information so that they can again, make that informed choice.
“But we were elected on this mandate, we’re doing the democratic thing.
“What’s undemocratic of course, would be for Alister Jack or the UK government to try to shut it down and deny democracy.”
Mr Yousaf gave his interview as hundreds of independence supporters marched through the streets of Ayr on Saturday.
The All Under One Banner (AUOB) march gathered at 12:30 at the Ayr Beach Park and moved through the town centre before rallying at Low Green.