There has been a mid-air collision between two small planes near Melbourne's Moorabbin Airport.

One of the planes landed safely but the other crashed and one of the pilots was killed.

The Civil Aviation Safety Authority (CASA) says a Cessna 150, which is a two-seater training plane, collided just after 12:30pm with a Piper Warrior, which seats four people.

The Cherokee landed safely at Moorabbin Airport but the Cessna crashed in a property near the corner of Dandenong and Warrigal Roads.

Witnesses say the Cessna crashed into the garage roof of a unit on Silver Street and burst into flames, killing the pilot.

Alex Mickham lives in the unit next door and was just 10 metres away when the plane came down.

"I didn't realise that it went right in the garage and it burst and the fire started. It was all red and I was in such shock that I got him out," Mr Mickham said.

Peter Gibson from the CASA said both planes were light training aircraft operated by the Royal Victorian Aero Club, which is a major flight training organisation.

He said Moorabbin Airport does have air traffic control but it is not clear if the planes were operating under their control or independently.

He said that would be examined as part of an investigation.

Cheltenham East Primary school, which is near the scene, has been shut down but police say the students are safe.