When he landed about 1pm, the pilot noticed a piece of metal - the "heat shield'' which protects the luggage pod from the exhaust - had come loose.
"The bang was the heat shield bending back on itself and hitting the pod,'' Mr Crawford said.
No-one was hurt and the plane had been repaired and was already back in the air.
"In hindsight it was a pretty minor incident but the pilot made the right decision to declare an emergency and to go to the right airport.''
The rest of the airline's fleet would be checked but did not need to be grounded, Mr Crawford said.
Marlborough Airport chief executive Dean Heiford said a full emergency had been declared with the Defence Force, Fire Service, police and airport staff put on standby.
"The aircraft landed safely, although rather hard, and is now sitting on the apron.
The airport shares its runways with the RNZAF's Woodbourne base.