The fire tore through a weatherboard building at Murchison East railway station shortly before 5pm on Wednesday.

Fire authorities and police will investigate whether the blaze was lit by an arsonist.

A man aged in his 50s was treated by paramedics at the scene for heat stroke, an ambulance spokesman said.

The building was fenced off as it is no longer in use, but the station is still operational for trains and buses between Shepparton and Melbourne.

Ten fire trucks and a helicopter from Shepparton were called in to battle the flames, which took more than an hour to bring under control.

"The blaze has extensively damaged the building," V/Line spokesman Colin Tyrus said.

"The platform itself has not been damaged, so services can still run, but demolition and removal of debris might be needed in the morning."

A train service from Melbourne to Shepparton has been given the all-clear to stop at Murchison East on Wednesday night, Mr Tyrus said.