Independent adviser Sir David Bell was tasked with investigating claims that Alex Salmond broke the code of conduct following a complaint by Labour MEP Catherine Stihler.
Sir David today reported that Mr Salmond had acted in accordance with the code but he has requested that the Scottish Government considers revising parts of the code which relate to legal advice.
He wrote: "I have not found you, or the Scottish Government, to have breached the Ministerial Code in respect of any complaints made by Ms Stihler.
"I have, though, recommended that the Scottish Government considers revising those parts of the code relating to legal advice."
Mr Salmond referred himself to an independent panel of advisers in October last year after a row erupted over the issue.
Earlier that month, Deputy First Minister Nicola Sturgeon revealed in the chamber that the SNP administration had only recently commissioned specific advice on Scotland`s position in the Europe.
The SNP has insisted that Scotland will automatically be accepted into the European Union (EU) in the event of independence.
Opposition politicians said the Government`s apparent confidence on continued EU entry created the impression that advice already existed.
They also pointed to comments made by Mr Salmond in an interview with the BBC's Andrew Neil where the First Minister appeared to suggest he had legal advice.
Ms Stihler had previously submitted a Freedom of Information request to try to ascertain what advice, if any, had been given to the Scottish Government.
Ministers took the case to the Court of Session to try to prevent the release of any information.
The legal challenge was dropped by ministers after Ms Sturgeon`s statement to Holyrood confirmed there was no existing specific advice.
Sir David examined five separate grounds of complaint from Ms Stihler, and in each case he found that the First Minister and the Scottish Government had acted in accordance with the code.
However, he concluded that he had commented at various points in the report on the "muddled and potentially confusing nature of Mr Salmond`s responses to Andrew Neil" during the interview, and on the lack of clarity in relation to provisions on Law Officers and legal advice contained in the code.
Sir David said the problems lay within the code itself and stated the current lack of clarity was unsatisfactory.
"More clearly-drafted provisions would help ministers explain their position to the Parliament, the media and the public on those occasions when, quite properly, they are not able to reveal or disclose information," he said.
Responding to the report, Mr Salmond said: "I would like to thank Sir David for his very thorough and detailed report, the findings of which clearly demonstrate that there was no breach of the Ministerial Code on this matter.
"I welcome the report which demonstrates that I and the rest of the Scottish Government acted entirely in accordance with the Scottish Ministerial Code.
"I also welcome his conclusion that the signing of the Edinburgh Agreement was the appropriate moment at which to seek specific legal advice on an independent Scotland's continued membership of the European Union.
"Sir David also recommends that the Scottish Government considers whether the section of its Ministerial Code relating to legal advice provided to ministers should be redrafted to make it clearer.
"That is a recommendation I am happy to accept and work will now be taken forward by Government officials with that aim in mind.
"This has been the sixth complaint to be referred to the independent panel of advisers I introduced in 2008 to rule on these matters.
"I am delighted that each complaint has been dismissed and the advisers concluded my ministers and I have acted entirely properly at all times."
But Scottish Labour's Paul Martin MSP said: "The man handpicked by the First Minister to look into the EU legal advice debacle has concluded that when asked whether he had legal advice Alex Salmond, and I quote, 'did not answer the question directly.'
"Worse than that he said Alex Salmond’s answers were muddled, incomplete and confused. This report has concluded that the Government’s position on the legal advice scandal ‘stretched credulity’.
"And these conclusions are in a report which the First Minister says clears him. Alex Salmond misses the point. The point isn't whether he broke a ministerial code which he writes, the point is did he mislead the people of Scotland when he said he had legal advice.
"He clearly did. Alex Salmond doesn't answer questions directly. Rather than tell the truth he employs muddle and confusion to try to mislead the people of Scotland.
"The First Minister got to pick the judge in this case and he got to pick the charges. And yet even in those circumstances Salmond is found to have evaded questions and used muddle and confusion.
"Yet bare-faced Salmond has the brass neck to crow that this report completely clears him.
"The truth is, as this report shows, you cannot trust the words which come out of Alex Salmond's mouth."
Catherine Stihler MEP said: "I find it strange that Sir David Bell has concluded that the First Minister was correct to wait until the Edinburgh Agreement before seeking legal advice on Scotland's place in the European Union.
"That looks like more of a post event alibi, than a real reasoning. The truth is the First Minister said he didn't need the section 30 order which he now calls the Edinburgh agreement. When the UK government first proposed such an agreement he suggested it was an affront to Scottish democracy.
"Alex Salmond has re-written history on this one and Sir David appears to have fallen for it.
"Reading this report it is difficult not conclude what we have said all along. Alex Salmond said he had legal advice on Scotland's relationship with the EU when he hadn't even sought it."
Scottish Conservative leader Ruth Davidson MSP said: "This was a sham process to brush off legitimate questions about the First Minister's conduct.
"Alex Salmond was caught out, and in response resorted to appointing the judge and jury for his own trial. Even then, two of the jurors walked away from having to give a verdict.
"The fact is, earlier this year he said the SNP had sought legal advice, only for his deputy to say months later it had not.
"This whole system needs to be looked at, never again should the First Minister be able to orchestrate his own inquiry into his own wrongdoing.
"Mr Salmond might think this puts him in the clear, but actually he comes out of it with even less credibility than he had before."
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