The full report by a senior finance executive into the long-term options for the publicly owned South Ayrshire hub is being withheld to protect commercially confidential information.
It has led to accusations that ministers are expecting "blind faith" from the public when it comes to justifying spending taxpayers' money.
Romain Py submitted his finished report two weeks ago on the future of the airport, which lost millions of pounds under its previous owners, following a review that took three months.
Although the full document is being withheld, Deputy First Minister Nicola Sturgeon is expected to report key findings to the parliament's Infrastructure Committee in June.
Mr Py's recommendations will also influence another Government document that will outline ministers' "strategic vision" for the troubled Ayrshire airport, which the Scottish Government bought for £1 last November.
But Labour's infrastructure spokesman James Kelly said it was unacceptable that Mr Py's report would not be made public.
He said: "So far at least £5m has been committed to Prestwick Airport and the public deserves to know how this money is being invested and when it will be returned to the public purse.
"The Scottish Government cannot justify keeping taxpayers in the dark when their money is being spent on a project with no clear strategy in place. They are asking people to put blind faith in their actions on Prestwick without being prepared to put all the facts on the table.
"Nicola Sturgeon has paid scant disregard to parliament on this issue. She needs to publish this report and come to parliament urgently so that there is a clear and transparent debate about the how the airport is being taken forward."
The chief executive of Edinburgh Airport, Gordon Dewar, recently claimed Government ownership of Prestwick was distorting competition in the Central Belt. Glasgow Airport chiefs are also said to be uneasy over the arrangement, while Glasgow Chamber of Commerce (GCC) has previously appealed for reassurance the takeover will not have a detrimental effect on Scotland's second-busiest airport.
GCC chief executive Stuart Patrick said Ms Sturgeon had assured the Chamber in March that, while they would not be able to see Mr Py's full report, the "strategic vision resulting from the report would be published".
Mr Patrick added: "Irrespective of the issue of commercial confidentiality, we are clear that the Scottish Government has said it is committed to sharing the strategic priorities that will result from the completion of the business plan. We wait for that as soon as is practically possible."
Alex Johnstone, Conservative transport spokesman and a member of Holyrood's Infrastructure Committee, said he expected Ms Sturgeon to provide the panel with a robust account of Mr Py's findings. He added: "We certainly need to know what's in that report so that we have a realistic view. We all want to see Prestwick return to the glory days, but the route between where we are now and that achievement is going to be a long and hard one."
The Scottish Government stepped in to save the airport from closure after New Zealand owner Infratil failed to find a commercial buyer. Accounts have since shown it was running at a pre-tax loss of £9.77m in the 12 months to March 31, 2014.
A Glasgow Airport spokesman said reassurances had been received last year that the Government's plans for Prestwick would not damage any other airport.
A spokesman for Transport Scotland said: "Our senior advisor has completed his work at Prestwick Airport and we are currently considering his recommendations. The Deputy First Minister has committed to providing the Scottish Parliament with a further update on progress at Prestwick Airport when she appears at the Infrastructure and Capital Investment Committee next month."