Joining the EU on the existing terms of the UK would simplify the process, but the Scottish Government's proposed time-frame of 18 months is "too ambitious", Holyrood's European and External Relations Committee was told.
Experts also told MSPs that while it is unlikely that member states would veto Scotland's membership, the country would face tough negotiations on issues such as the budget, agricultural policy and security and justice.
The committee was taking evidence from a trio of academics who have been examining the impact of independence as part of the Economic and Social Research Council (ESRC) programme.
It is just over a week since the Scottish Government published its White Paper which outlines its proposals for membership of organisations such as the EU and Nato.
The Government asserts that Scotland would join the EU as part of a transition process, with negotiations taking place from within the organisation in the period between a Yes vote in September next year and Scotland becoming independent in March 2016.
Professor Michael Keating, director at the ESRC Scottish Centre on Constitutional Change, backed this view but said a time-frame of two years or more is more realistic.
He said: "In the last few months we have made a lot of progress on this issue to the extent of saying there doesn't seem to be an issue of principle, and there doesn't seem to be a legal issue on this. But there are huge practical difficulties to be overcome.
"So it is the details of the negotiation that are going to be the difficulties."
Prof Keating was joined at the committee by Professor Stephen Tierney, director of the Edinburgh Centre for Constitutional Law, who has examined the legal aspects of EU membership, and Dr Colin Fleming, also from the ESRC Scottish Centre on Constitutional Change, who has studied defence and security in relation to independence.
They agree that it would not be in the interests of any country for Scotland to be outside the EU for any period of time, due to the high level of disruption this would cause.
Prof Keating said: "Largely the interests of the rest of the UK would be to make sure that Scotland did not remain outside (the EU) for any period of time.
"None of the member states have threatened to veto. Since some of these member states would be very unhappy about Scottish independence, they might be unco-operative and they might try to increase the price.
"It's not a question of vetos, it's a question of the tough negotiations and how strong Scotland's position would be to get the terms it might want."
Prof Keating said entering the EU on "existing terms simplifies matters because you already have a template there".
He said: "If Scotland wanted to renegotiate its terms ... that would be much more complicated."
There would be "no question of being forced into Schengen", Europe's borderless area, while no state has ever been obliged to join the euro against its will.
But he warned of more difficult areas of negotiation.
"The budget would be a problem. Financial details would be a problem. Things like the agricultural policy - these would be problematic. Then details of things like security and justice ... that would be problematic."
Prof Keating also commented on Scotland's future within the EU.
"I think a much more difficult and much more important issue is where an independent Scotland would go within the European Union. We can talk about the euro. We can talk about the Schengen area. I argue that we would not have to adopt those immediately.
"But in the long run, Scotland would have to decide whether it was going to cling to the rest of the United Kingdom which seems to be moving away from Europe.
"I'm looking for a vision of Scotland in Europe, a vision of what kind of Europe Scotland wants ... and I don't see that in the White Paper."
Commenting on the legalities of accession, Prof Tierney said that while article 49 is the standard process for new memberships, the Government's proposal to use article 48 - a more simple process - seems to be "a plausible route".
Turning to defence, Dr Fleming said: "I think the defence blueprint in the White Paper is a sensible one and gives us a bit of detail, as much as it can, pre-negotiations.
"In terms of Nato membership, defence structures and commitments to personnel, the Scottish Government is trying to reassure the Scottish people, and also the rest of the UK and potential allies in the future, that it takes its defence responsibilities seriously. I think that does come across."
The removal of Trident nuclear weapons from Scotland within a period of seven to 12 years is "a realistic framework to move on".