Investigations were under way on Thursday morning after the routine freight flight went awry, Wagga Air Centre’s managing director Chris Cabot said.

The Sydney-based pilot was the lone traveller on board the twin-piston Piper Navajo when issues with the landing gear hit just short of Bankstown.

“(It was) a regular freight run that we complete 250 days a year to Sydney from western NSW and the pilot followed all procedures,” Mr Cabot said.

“He landed safely (and) the aircraft sustained some damage, but it’s repairable. He really fell back on his training.”

The light aircraft left Young around 6pm and ran into trouble over western Sydney.

It eventually landed around 7.40pm, 50 minutes after its scheduled arrival time.

It is “a bit early to speculate” on what went wrong, Mr Cabot said, but it’s believed a mechanical failure led to the belly landing.

“We have a series of systems we have to try (and) emergency back-up systems to try to get the undercarriage down on the aircraft manually, and those systems failed to work,” Mr Cabot said.

The Australian Transport Safety Bureau (ATSB) and Civil Aviation Safety Authority will investigate the matter.

The pilot, who escaped injury in the emergency landing, is back on the flight deck today.

“He’s fine,” Mr Cabot said.

“As part of our safety management systems he was drug and alcohol tested last night and came up clean, and he’s back on duty today after some counselling.”

According to flight logs, the aircraft left Bankstown airport shortly after 6.30am on Wednesday for the daily freight trip.