The move follows a meeting between Enterprise Minister Iain Gray and senior executives of Scotland's economic development agency.
Mr Gray summoned Scottish Enterprise chief executive Robert Crawford and its chairman Sir Ian Robinson to a showdown meeting over concerns that the body had conducted a political battle against the Tories.
Scottish Enterprise has accepted that it should not act, or be seen to act, in a party political manner and its executives apologised for any confusion.
The row erupted after BBC Scotland revealed the details of an internal Scottish Enterprise e-mail which proposed a "head-on attack" on Tory criticism of the body - a breach of its duty to be non-political.
Following the meeting in Edinburgh, which lasted an hour and three-quarters, Mr Crawford emerged to say that Mr Gray had accepted that the e-mail had been "misinterpreted".
He added: "The tenor of the memo was misunderstood and we apologised for that and the minister accepted that.
"We already made it clear yesterday that the memo was misinterpreted as an attack on the Conservatives, which it certainly was not and we apologised for that misinterpretation.
Unambiguous guidelines
"It was never an attack on the Conservatives or indeed any other party."
In a joint statement issued minutes later, the three men admitted that the wording of the e-mail had been "regrettable".
It went on to say that those working for quangos, or Non-Departmental Public Bodies (NDPBs), should have "clear and unambiguous guidelines covering their conduct", as civil servants already do.
Speaking afterwards, Mr Gray said it was important that guidelines existed so that quango employees know what is and what is not acceptable.
Scottish Tory Leader David McLetchie later met Mr Gray to discuss the matter and voiced approval at plans for a code of conduct to be drawn up by Muir Russell, head of the civil service.
He said the Scottish Enterprise had been "out of order" in its actions during the row but he had been given an assurance that the matter had now come to an end.
Mr McLetchie said: "I hope that very clear guidelines emerge from Muir Russell and that these are adhered to by Scottish Enterprise, all the local boards and the other quangos to which they apply.
"If that is done, I think something positive will have come out of this whole affair.
"I just think it was unnecessary and irresponsible for Scottish Enterprise to act in this manner in the first place."
Scottish National Party enterprise spokesman Andrew Wilson said: "The truth is that Mr Gray must have known what was going on.
"He must have known about the e-mail and at least one political article which has appeared in print.
"Big questions remain unanswered, why did Mr Gray not intervene earlier and where else is such behaviour taking place?"