Enterprise Minister Ian Gray has asked Scotland's auditor general to investigate the use of consultancies by Scottish Enterprise.
Concerns have been raised about the agency
The move follows a BBC Scotland investigation and press reports about the agency's financial management and use of European funds.
There were allegations that the agency had spent millions of pounds on hiring private consultants, had blundered in applying for European funds and was running into trouble on major projects.
Chief executive Robert Crawford has denied all the allegations but the controversy has not died down.
On Monday, Scottish Tories wrote to the Auditor General, Robert Black, asking for a far-reaching and independent inquiry.
The Scottish Executive has now confirmed that officials in Mr Gray's office wrote to Mr Black on the same day requesting an examination of Scottish Enterprise's use of consultants.
However, Mr Gray stressed that he has been taken aback by the controversy and continued to express confidence in Scottish Enterprise.
Iain Gray: Surprised by controversy
He said: "I do find it a little surprising. I've said before that we have confidence in our economic strategy and in Scottish Enterprise's role in taking that forward and indeed the first minister said exactly the same thing last night."
The Tories have welcomed the move but said the inquiry should be a root and branch affair and should not be confined to one area of the agency operations.
Deputy Leader Annabel Goldie said: "Of course it's a start but it doesn't go far enough because there are clearly widespread concerns about allegations concerning laxity of management and slippage of programmes.
"These are very, very important areas to be investigated and the Conservatives have requested that these areas, in addition to the element of consultancy fees, be looked at."