The airline began flights from the airport three weeks ago
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The company that runs Manston airport has raised more than £5m to acquire a controlling stake in the budget airline operating from the airport.
PlaneStation already owns 30% of EUjet, which began flights from Kent International Airport three weeks ago.
The deal is subject to approval by the Civil Aviation Authority.
EUjet chief executive, PJ McGoldrick, said the move was a result of the airline's success, but PlaneStation has said job cuts could follow.
Chief executive for the airport operator, Martin May, said: "There will be a tightening up of the operation."
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The business will be determined, at the end of the day, by the travelling public - if we get support, it will be a success
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He told BBC Radio Kent there were elements of cost in both operations and that "some jobs will go".
Mr McGoldrick said the business depended on passengers.
"There's not two entities trying to make a profit out of each passenger now, there's one and that helps us," he said.
"Nothing has gone wrong. Everything has gone right.
"The business will be determined, at the end of the day, by the travelling public.
"If we get support, it will be a success."