Rosemary Agnew, Scotland's Information Commissioner, pulled away from legal action after the SNP complied with a demand for the sensitive paperwork.
In 2012, the Government was asked under freedom of information legislation for material relating to whether an independent Scotland would be required to sign up to the Euro and the Schengen agreement, which relates to freedom of travel.
The requests also covered whether a separate Scotland would retain any of the UK's budget rebate and other EU-related issues.
The Government said the much of the information was exempt from disclosure and Ms Agnew, who adjudicates on such disputes, was notified of the disagreement.
Part of the investigation process involves the relevant public body handing over the requested information to Agnew, so she can make an informed decision.
However, although the Commissioner asked for the EU information in November 2012, by March 2013 the Government had not given her the documents.
She issued the government with a legal demand that must be heeded.
Following her investigation, Ms Agnew concluded that Ministers were entitled to withhold the remaining information.
A Scottish Government spokesperson said: "We regret the delays in locating all the information on this occasion. This was due to a combination of factors, including staff illness and changes."