There were four crew and no passengers on board when the hard landing occurred on Sunday afternoon.
It triggered emergency procedures at the airport and has forced the runway to close for the rest of the day.
Several flights have been redirected to Belfast International Airport.
The airline operating the flight said the incident was a result of adverse weather conditions, which have been disrupting travel across the UK.
A Belfast City Airport spokesperson said: "At around 16.00 today, Sunday Dec 22, an Aer Lingus regional flight, operated by Emerald Airlines, had an incident on landing at Belfast City Airport.
"This was a positioning flight with no passengers but four crew members on board."
"The airport's emergency procedures were enacted.
"The runway is currently closed and will be for the rest of the day. Passengers are asked to contact their airline."
A spokesperson from Emerald Airlines said: "An Emerald Airlines positioning flight, EA701P, with no passengers on board, flying from Edinburgh to Belfast City Airport, Dec 22 2024, experienced a hard landing upon arriving into Belfast City Airport due to adverse weather conditions."
A spokesperson for Belfast International Airport said: "Following the incident at Belfast City Airport this afternoon we have taken four diverted flights.
"As we already had a heavier schedule than usual, we are now, with these additional flights, close to capacity so we are limited in how many more redirected flights we can take this evening, however we will continue to support where possible.
"Our website will carry the most up-to-date information for arrivals and departures and if anyone has any queries they should be directed to the airlines.
"Given the circumstances, our teams on the ground are working to help these additional flights as quickly as possible.
"We would ask for passengers' patience as we support each additional flight."