At a fringe meeting on Europe, Michael Moore, the Scottish Secretary, said: "There is, of course, a clear parallel between those who want Scotland to leave the UK and those who want the UK to leave the EU.
"For both the Nationalists and the Eurosceptics, there is a hard need to assert a specific sense of national identity; that need over-rides facts. The First Minister has said that nationhood rather than economics is at the heart of Scottish nationalism and Eurosceptics place sovereignty rather than jobs, trade or family finances at the centre of their case.
"But the arguments in favour of the UK family and the EU family are highly rational and very similar," he said.
The Secretary of State argued that both these families were formed out of a growing sense of cross-border identity and the realisation that cross-border co-operation benefited everyone.
"Whether we talk about the need for a free market, movement of people, or big and specific challenges like climate change, the answer is in partnership not separation," he declared.
"For all the noise that these two groups make and for all they would claim to be in opposition, Nationalists and Eurosceptics pull in tandem and stretch to breaking point our national interest."
Mr Moore added: "Liberals are comfortable in our identity - Scottish, British, Europe- and we will continue to make the case for co-operation not separation."
The SNP branded Mr Moore's remarks "absurd".
A spokeswoman said: "It is the Tory-led government he is helping to prop up that is dancing to Ukip's tune, which is utterly unrepresentative of Scotland, where Ukip have never once even saved their deposit in an election; and his own party are now pandering to Ukip by moving towards backing a referendum to exit the EU."