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Ryanair is withdrawing its Belfast to East Midlands route from October.
The company said it is withdrawing a total of five routes to East Midlands, Stansted, Liverpool, Bristol and Glasgow Prestwick.
Airport spokeswoman Katy Best said she was extremely disappointed.
"Ryanair will cease services from Belfast City Airport on 31 October 2010. Passengers are advised to check with Ryanair for bookings made after that date," she said.
The airline has supported the George Best Belfast City Airport's bid to secure a runway extension at its site in the east of the city.
It has been running on a reduced passenger load since its operations were established in October 2007. There are also restrictions on night-time flying.
A public inquiry was launched into the runway extension after vociferous opposition from local residents. It was suspended earlier this summer.
Ms Best said: "We are obviously disappointed at Ryanair's decision; the airline had provided five successful routes from Belfast City Airport.
"However, passenger figures had proved that there was significant demand for the routes operated by Ryanair and I am confident that we can attract other airlines to fill the void.
"Recent significant and continuing private investment by the airport's owner has made Belfast City Airport an attractive proposition for passengers and airlines alike."