Alistair Carmichael also warned that although countries like Spain and Croatia may not block Scottish entry, they are likely make negotiations difficult.
The Scottish Secretary was giving evidence before MSPs on Holyrood’s European and External Affairs committee today which is conducting an inquiry into the prospect of Scotland joining the EU after independence.
The Liberal Democrat minister said that as part of the UK Scotland enjoys a multi-million pound rebate on the EU Budget contribution, an opt-out from the Schengen open borders deal and is exempt from the euro single currency.
“If we are to go back into the European Union, do we do it as I think the Croation ambassador said, where you take the terms and conditions that we’re offered which paraphrasing him were more or less on a `take it or leave it’ basis,?” he added.
“Or are we going to insist on negotiating the opt-outs that we currently have. That will not be an easy negotiation.”
He added; “If you accept the Croation ambassador’s view that an independent Scotland takes what you might regard as the `off the shelf’ terms and conditions of entry then that means we’re put in a significantly worse condition than we currently are.”
The SNP Government says that Scotland would be able to renegotiate itsmembership of the EU from through alterations to Article 48 of the treaties - and could achieve this inside 18 months by time Scotland becomes officially independent in March 2016.
But European leaders like EC President Jose Manuel Barroso and European Council head Herman Van Rompuy say a Yes vote would leave Scotland outside the EU and it must re-apply to join through an Article 49 negotiation.
Mr Carmichael said: “I don’t see why they would seek to use Article 48 when Article 49 is there and its very clear.”
But he added that even if Article 48 was used, there would still need to be negotiations to ensure that Scotland is compliant with all the existing EU charters.
“In that respect, I’ve always felt that 18 months was an ambitious timescale, especially as we don’t know some of the most fundamental questions with regard to the currency and the central bank.”