The comment followed a letter to the SNP government from Chief Secretary to the Treasury Danny Alexander.
In it he said uncertainty over Scotland's future was damaging the UK economy as a whole.
Mr Swinney said he was happy to have an evidence-based debate, but there was no evidence coming from the coalition.
In an interview on BBC Radio Scotland's Good Morning Scotland programme, Mr Swinney said: "The United Kingdom government is now becoming ever more hysterical in how it responds to this particular issue [independence]."
The SNP minister's response is the latest in a series of political comments on Scotland's economy.
Last week, the Chancellor George Osborne claimed instability caused by the planned referendum on independence was damaging investment in Scotland.Mr Alexander has continued the war of words between Westminster and Holyrood by sending a letter to Mr Swinney in which he said the SNP's core policy commitment was causing "real uncertainty".
In an interview with BBC Radio Scotland's Good Morning Scotland programme, Mr Alexander said both City Group and CBI Scotland had expressed concerns about the "uncertainty" created by the issue of an independence referendum.
He added: "Most strikingly of all last week we heard from Transport Scotland, which is one of the Scottish government's own quangos, saying that they thought they would have to issue shorter rail franchises in future because of the constitutional uncertainty.
"The reason why governments are moving towards longer rail franchises is because that is the way to get more investment in railways, it is the way to keep fares down and so it is quite extraordinary in a sense that you've got one of the Scottish government's own organisation themselves saying they see this as an issue."
Mr Alexander told presenter Gary Robertson that he thought Scotland was a "brilliant place to invest and we all need to see economic growth across the whole of the UK".
The Chief Secretary to the Treasury added: "If Scotland exceeds it helps the whole of the UK. If Scotland is dragged down by this uncertainty then that affects the whole of the UK too."
Finance Secretary John Swinney, speaking on the same programme, said: "What I asked the chancellor was a simple set of questions about what had motivated him to put out a message that tried to sabotage the Scottish economy.
"I didn't get a reply from the chancellor, I got a set of other answers from the chief secretary to the treasury, who cannot possibly know what the chancellor was thinking about when he set out his views.
"I think at the very least the chancellor should reply directly to the accusation that I put to him."
The SNP has pledged to carry out a referendum on independence in the latter part of its five-year term.