The Scotsman has also learned that former chief executive Stewart Adams, who had stayed on to help with the sale after stepping down from his post in May, has now left the airport.
Ministers announced an undisclosed new preferred bidder for the South Ayrshire complex had been chosen in February, five months after its sale to the original chosen bidder – believed to be Glasgow Airport owner AGS – fell through.
French firm Vinci, which runs Gatwick and Belfast International airports and has been linked to the sale, yesterday again declined to say whether it was involved.
Mr Adams, who was replaced by deputy chief executive and chief financial officer Ian Forgie in May, stepped down as a director on Thursday.
Transport Scotland said the process of returning the airport to the private sector was ongoing, but “decisions have still to be taken in relation to the prospective sale of the business”.
It is understood that might relate to whether a buyer would take on the £43.4 million loaned by the Scottish Government to keep the airport going since it was bought for a nominal £1 in 2013 to avert closure by New Zealand owners Infratil and hundreds of job losses.
Transport Scotland said the loan had still to be repaid.
One source said: “My understanding is that the preferred bidder is still waiting for an answer on a new lower bid.”
Another said: "I have heard the Scottish Government is swithering as to whether they really want to do the deal and worried about the political optics.
"That makes me speculate that the deal is very low value – who is going to buy an airport for a high price with all the impact Covid has had on the sector?"
Scottish Conservatives transport spokesperson Graham Simpson said: “It’s time the SNP came clean on what’s going on here.
"We know there was a preferred bidder. We also know there was a hitch.
“If there has been a new offer from the airport and the government has decided not to sell for some as-yet-unexplained reason, then we should be told.
“It looks like yet more dithering and delay from the SNP.”
The Scottish Government said the value of the loan on Transport Scotland’s books had been “impaired” to recognise the risk associated with “expected credit losses”, but it had not been written off and the full value plus accrued interest remained repayable.
A spokesperson said: “Glasgow Prestwick Airport is operated on a commercial basis and at arm’s length from the Scottish Government.
"Ministers do not intervene in the commercial discussions at the airport.
“The process to return the airport to the private sector continues and decisions have still to be taken in relation to the prospective sale of the business.
"We have committed to updating Parliament on the sale process at the appropriate stage and to protect the integrity of the process we will not be making any further comment at this time.”
A spokesperson for Glasgow Prestwick Airport said: “We can confirm that after four successful years at the helm, Stewart Adams has now formally left the airport and we wish him well.”