The announcement by Deputy First Minister Nicola Sturgeon follows concerted criticism from opposition parties about the SNP's attempts to keep the information under wraps.
It also effectively ends a potentially expensive legal challenge against a ruling by Information Commissioner Rosemary Agnew who ordered the Government to reveal whether advice was sought.
Ms Sturgeon made the comment during a statement at the Scottish Parliament just over a week since Prime Minister David Cameron visited Edinburgh to sign off a deal ensuring a legal and decisive referendum in 2014.
"In light of the Edinburgh agreement, by which both governments have agreed the process for Scotland to achieve independence, I can confirm that the (Scottish) Government has now commissioned specific legal advice from our law officers on the position of Scotland within the European Union if independence is achieved through this process," she said.
"The Scottish Government has previously cited opinions from a number of eminent legal authorities, past and present, in support of its view that an independent Scotland will continue in membership of the European Union but has not sought specific legal advice.
"However, as the Edinburgh agreement provides the exact context of the process of obtaining independence, we now have the basis on which specific legal advice can be sought."
She said the views of those eminent authorities, which the Scottish Government has so far relied on, will continue to be "highly relevant".
She told parliament: "Given that my statement today answers the ruling of the Information Commissioner on the existence of legal advice, there is now no need for the Government to pursue an appeal against this ruling in this specific case and I have asked our lawyers to advise the court accordingly and to ask that the appeal be dismissed."
The SNP insists that Scotland will automatically be accepted into the EU, while opponents say it would have to reapply and lose the UK's existing rights and opt-outs.
Tory leader Ruth Davidson turned on the Government after it admitted that ministers had yet to take legal advice on the key issue of membership of the European Union.
"We find out today, despite desperate claims of knowing the answer, despite thousands of pounds in taxpayers' money spent in courtrooms to keep information from the Scottish people, the SNP have never taken advice on a separate Scotland's place in the European Union.
"They don't know whether we would be spending pounds or euros. The Deputy First Minister doesn't know.
"Monetary policy, EU membership: when will she stop trying to hoodwink the public on the big issues. Scotland needs to know."
She demanded that the Government publishes the "actual advice" it receives so that "Scotland has the information it needs to make this historic decision".
Labour's Jackie Baillie also turned on the Government, demanding to know how much cash was spent pursuing the court case against the Information Commissioner.
"Can I ask how much taxpayers' money the Government has spent on a court case to hide information on legal advice on the European Union; legal advice which wasn't even commissioned, legal advice which doesn't exist."
Ms Sturgeon said expenses so far totalled £3,960, although this is not "an absolutely final figure" and pledged to update parliament on the final cost as soon as it is available.
Liberal Democrat leader Willie Rennie also raised the European issue, telling Ms Sturgeon that he can "feel her embarrassment".
The Lib Dem recalled: "The First Minister said his White Paper would be consistent with the legal advice. She's had to tell us he hasn't got any, it was all imaginary."
Meanwhile Labour MSP Richard Baker demanded to know how the Deputy First Minister could reveal the "existence or non-existence of legal advice" under the ministerial code, which normally precludes this.
Ms Sturgeon said she received specific permission from Scotland's top law officer, Lord Advocate Frank Mulholland on the matter.
"I have sought and received the specific permission of the Lord Advocate to share this information with Parliament today. That means I am giving Parliament this information entirely consistently with the ministerial code," she said.
Ms Sturgeon asked to make the statement at Holyrood on the first day back from recess.
It was the first available opportunity to update MSPs on the agreement struck between the British and Scottish governments on the staging of the referendum.
The deal paves the way for both parliaments to agree a technical section 30 order giving the Scottish Parliament power to legislate for the date of the referendum, whether to reduce the voting age to 16, the wording of the question, campaign finance rules and the conduct of the referendum.
The statement coincided with delayed publication of the results of the Scottish public consultation on the staging of the ballot.
The consultation ran from January 5 to May 11, leading to complaints that the deal in Edinburgh was made without full transparency.
Issues put to the public included the proposed timetable, whether there should be weekend voting, who should oversee the running of the referendum and what the spending limits should be.
Information Commissioner Rosemary Agnew said she is "not minded" to oppose the request to drop the appeal, which followed an initial demand by Labour MEP Catherine Stihler for details on legal advice.
"We welcome the Cabinet Secretary's statement today which indicated that the Scottish Government intends to seek leave to abandon its appeal against decision 111/2012 Catherine Stihler MEP and the Scottish ministers," said Ms Agnew.
"The Cabinet Secretary confirmed that the Government had not, at the time of Ms Stihler's request, received legal advice. We have consulted with our legal advisers and are not minded to oppose the request."
Ms Stihler said: "The inconvenient truth is the SNP have lied about possessing specific legal advice on EU membership and it took them until today to admit this.
"When I attended the Court of Session in September the Scottish Government must have known that their legal advice was just a blank sheet of paper. Thousands of pounds later and now we are told they are seeking legal advice.
"You couldn't make it up. It's lies, lies and more damned lies."
Meanwhile, results of the delayed referendum consultation suggest most people are in favour of a single question and agree with proposals to lower the voting age to 16.
Analysis of the survey shows opinion is broadly in tune with the deal struck in Edinburgh last week between Prime Minister David Cameron and First Minister Alex Salmond, which paves the way for a legally binding referendum in 2014.
A report on the 26,219 responses made to the consultation has been made public by Ms Sturgeon who led negotiations for the Scottish Government.
In her statement to MSPs, she said: "The analysis indicates broad support for the Government's proposals on the question, the timing of the referendum, votes for 16 and 17-year-olds, and spending limits. Opinion is split on the issue of voting on Saturdays."
Almost two-thirds (63%) of respondents agreed with the Scottish Government's proposed question: "Do you agree that Scotland should be an independent country?"
Only one-quarter called for the inclusion of a second option for more devolved power short of independence. That option, known as devo max, was opposed from the start by the UK Government.
The proposed timetable, which would see the question put to the people in autumn 2014, was backed by 59% of those taking part in the consultation.
One-third of respondents agreed with the idea of holding the vote on a Saturday, while just over half (53%) backed calls to extend the ballot to people as young as 16.
Ms Sturgeon said the responses will "influence and inform" the final Bill presented to Parliament.
The Electoral Commission will play an "important role" in formulating the question, she said, while also giving advice on spending limits to ensure a "fair contest and a level playing field".
The Scottish Parliament later revealed that a committee is likely to be set up to scrutinise the technical section 30 order, designed to ensure the legally binding referendum.
The committee is expected to involve six SNP MSPs, two Labour MSPs, former Tory leader Annabel Goldie, former Liberal Democrat leader Tavish Scott and Green party co-convener Patrick Harvie.