A source at the Mombasa airport who sought anonymity told The Star that none of the four soldiers on board was injured.
"It happened at the far end near the military base," the source said.
Two other aircraft were diverted to Nairobi as a result of the mishap as the airport only has one runway.
The Fly 540 and AirRwanda planes were about to land.
According to Capital News, Passengers were stranded at the Moi International Airport in Mombasa Wednesday morning after operations came to a standstill when a military plane developed mechanical on the runway.
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According to airport officials, the plane burst all its tyres at about 9am while taking off affecting the landing and departure of planes at the airport.
Kenya Airports Authority (KAA) officials spent the better part of the day clearing the runway.
KAA and Kenya Airways engineers were mobilised to carry out the task as KDF launched investigations into the incident.
Several passengers were stranded as a number of airlines canceled scheduled flights.
But the source said no other flights would be interrupted.