A three-day search for a man wanted in two states has ended with Victoria Police finding him hiding in a wombat hole in the state's remote far east Gippsland region.

Detectives say police dogs tracked the 43-year-old man to the hole next to a river at Genoa, near Mallacoota.

The man had been on the run since Friday afternoon after he fled from highway patrol officers who pulled him over at Cann River.

Local police say the man is wanted in Victoria and New South Wales on charges ranging from driving offences to assault, and numerous warrants have been issued for his arrest.

A police helicopter and the dog squad joined the hunt for him in rugged parts of Gippsland before it ended at the wombat hole.

It is not clear how long the man had been hiding in the hole.

He will face court later this week.