Hugo Swire said there was no basis to SNP claims that because Scots were already EU citizens by virtue of being British, they would stay in the EU if Scotland became independent following a referendum in 2014.
Mr Swire admitted the Foreign Office had not discussed the implications with the Scottish Government because it did not believe in "pre-negotiation" in advance of the referendum - but he said civil servants in Whitehall were analysing the legal issues and "engaging with legal experts".
Scottish First Minister Alex Salmond has faced accusations he was misleading about getting his own legal advice on EU membership after suggesting on television the advice was clear but could not be released - before later admitting no advice had been sought.
Speaking in a Westminster Hall debate, Mr Swire said the UK had over decades negotiated its own exemptions and relationship with the European Union - including opt outs from the euro and the Schengen area rules, while also securing a rebate.
He said: "If Scotland left the UK and applied to join the EU, these would be subject to negotiation and there is no guarantee whatsoever Scotland would obtain any of these rights the UK currently enjoys.
"It is precisely the UK's weight and influence as one of the EU's largest member states that allows it to negotiate such arrangements.
"Scotland, like England, Wales and Northern Ireland derives enormous benefit from it.
"The fact is, if Scotland became independent, everything would change.
"Independence is not simply an extension of the devolution arrangements which have worked so well.
"It is a fundamental state... and irreversible step.
"As set out in the FCO memorandum to the Foreign Affairs Committee, independence would create a new state.
"One which would have to take its place on an already crowded international stage... Scotland would start afresh."
Mr Swire said the "overwhelming weight of international legal precedent" underlined the point - highlighting Russia after the break up of the USSR, India and Pakistan, Eritrea and Ethiopia, and Sudan and South Sudan.
And the minister added: "(An independent Scotland) could not assert membership of any organisation.
"There have been no discussions with the Scottish Government on this issue, we are not in the business of pre-negotiation, because we do not believe Scotland will vote for independence."
Speaking earlier in the debate, Pete Wishart, SNP MP for Perth and North Perthshire, insisted it was wrong to suggest an independent Scotland would have to negotiate EU membership - because it was already a member.
He said: "We remain members of the EU because the UK took us into the European Union in 1973.
"When Scotland secures its independence, the Act of Union will fall and there will be two successor states.
"Whatever happens to an independent Scotland will happen to the rest of the United Kingdom - that's what happened in Czechoslovakia."
Mr Wishart said the only country ever to have left the European Union was Greenland - a process he said took two years of detailed negotiation after Greenland actively voted to leave - and there was no precedent or procedure to kick out a member state.
And he told MPs the biggest threat to Scots being forced out of the EU came not from the SNP but the Conservative eurosceptics.
He said: "The threat comes from the Westminster Tories.
"They are at it again.
"They are even prepared to defeat their Government to ensure they get this country out of Europe.
"(Bookies) are offering odds of 6-1, which I think are very generous, that the UK will be out of the EU by 2020.
"That is the threat to Scotland's EU membership."
The Westminster Hall debate was called by Labour's Ann McKechin, MP for Glasgow North, who said: "Every time the Scottish Government have been asked about the question of status, they have sought to give a firm impression continued membership was guaranteed and no real material change in the membership of the nation would result.
"The SNP argue when they make their contentions on EU membership, they are speaking about evidence from a variety of experts.
"But that is not the same as legal advice and they know the difference... and there are just as many eminent people who disagree with those expert opinions - including no less a person than the current European Union president (Herman Van Rompuy)."