Home Secretary John Reid has claimed independence would make Scotland and the UK "weaker" in the war against global terrorism.
In a series of newspaper interviews, he said Scotland could be left defenceless against groups such as al-Qaeda.
But his claims met with an angry response from Scottish National Party leader Alex Salmond.
The MP said the comments were "an inept attempt at slandering" the SNP from "a serial offender in blundering".
Mr Reid's comments follow his attack on the SNP at Labour's Scottish conference, when he said the party was "not fit for purpose".
In newspaper interviews, the home secretary claimed anti-terrorism measures would be reduced if Scotland broke away from the UK.
"The SNP will not be taking any lessons in preserving this country's security from this London minister who is, in his own words, not fit for purpose"
He also warned that Scotland could be left defenceless without the protection of MI5 and MI6.
And he said the idea that terrorists would distinguish between Scotland and England was "woefully unfit for the challenges that face the modern Scotland".
However, Mr Salmond pointed to a recent poll commissioned by the SNP which claimed three quarters of Scots thought the war in Iraq had not made Scotland safer.
"Not only has Mr Reid personally failed in his own duty to protect the public, but his London Labour's government's war in Iraq has also added to the security problems facing the country," he said.
"It is this Labour government who has failed to meet Scotland's security needs, and this home secretary who has presided over their most recent failures.
"I think that we have to accept that it is dangerous to play politics with terrorism"
"The SNP will not be taking any lessons in preserving this country's security from this London minister who is, in his own words, not fit for purpose."
Speaking on the BBC's Politics Show, Paul Wilkinson, Professor of International Relations at St Andrews University, agreed with Mr Reid that al-Qaeda would not distinguish between Scots and people from any other part of the UK.
But he added: "I think it would be foolish to assume that it is impossible for a small independent country to improve its own anti-terrorism measures to incorporate linkages with the EU and with other countries in the general sharing of intelligence, which is so vital.
"I'm quite sure that whoever is in power in Scotland is going to have both the responsibility and opportunity to join in the very best level of international co-operation, which is a crucial part of protecting against a trans-national terrorist organisation like al-Qaeda."
He said it was "dangerous" for Mr Reid to imply that independence would disrupt the scale of the intelligence-gathering effort.
"I think that we have to accept that it is dangerous to play politics with terrorism," he added.
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