The claim breaks an unwritten “Team Scotland” convention that airports do not try to take advantage by criticising each other.
However, Edinburgh has accused Prestwick of again comparing itself favourably against other Scottish airports, at an international aviation conference last week.
Prestwick chief executive Ron Smith told Holyrood’s rural affairs and connectivity committee last month that the Ayrshire airport was attractive to airlines because of its lack of congestion compared to Edinburgh and Glasgow.
He said: “We can give them not only the landings and slots that they require but their preferred timings for the slots.
“It is not for me to say, but I think that it would be pretty difficult today for an airline to get a new slot at its preferred time at Edinburgh airport.
“We have that advantage, so we are trying to exploit it as part of building the attractiveness of Glasgow Prestwick to the airlines.”
The comments angered Edinburgh Airport, which accused Mr Smith of making “unfounded statements without prior checks”.
Mr Smith has now apologised to the airport and the committee, admitting he had “wrongly used a competing airport as a hypothetical example”.
He told MSPs: “It was inappropriate of me to do so and I do not have the information on the inner workings of Edinburgh Airport to have made this comment.
“This statement should carry no weight and be no reflection of the ability of Edinburgh to continue to grow.”
Mr Smith said his focus was on rebuilding Prestwick by highlighting its own merits.
He said: “As an advocate of a Team Scotland approach, we are committed in doing this on our own merits and not through commenting on our competitors.
“Our chair [Andrew Miller] has apologised in writing to Edinburgh Airport.”
However, Prestwick further claimed advantage at an International Air Transport Association conference in Kuala Lumpur.
Business development manager Mike Stewart said: “Unlike other airports in Scotland, we can offer 24/7 operations and are able to accommodate any aircraft.”
An Edinburgh Airport spokesman said: “It appears that Prestwick’s apology to the committee is a hollow one.
“Again, they have been found promoting themselves on the back of unfounded claims about other Scottish airports. Why they feel they need to do this is bemusing. This is not the Team Scotland approach that we expect.”
But Prestwick this time remained unabashed. Its spokeswoman said: “Where we have something to offer that a competing airport cannot, we will highlight this - as any other commercial organisation would. Promoting the unique capability that we offer could help to secure new connections for Scotland.”