Two directors of a high-profile real estate franchise have been charged after police allegedly uncovered cannabis crops in a number of residential properties in Melbourne's north.

The joint owners of Barry Plant Real Estate's Epping branch and another man were charged with cultivating and trafficking a large commercial quantity of drugs after police executed 16 search warrants at properties in Epping, Wollert, South Morang and Mill Park, seizing about 3000 plants.

Barry Plant chief executive Mike McCarthy said the company, which operates independently of the Epping franchise, was ''shocked and dismayed'' at the pair's alleged activities, believed to have been carried out at properties they managed.

Mr McCarthy said: ''We've taken immediate steps to contact the property owners. This was an isolated office, it's owned by these two individuals, they have nothing to do with the operation of other Barry Plant offices apart from Thomastown branch, which they also manage.''

Mr McCarthy said the accused men were ''professing their innocence'' and had co-operated with Barry Plant's head office.

Whittlesea Crime Investigation Unit detectives along with the Mill Park Divisional Response Unit executed the search warrants as part of an ongoing investigation, police said.

A 52-year-old Greenvale man and a 52-year-old Lalor man have been charged with cultivation and trafficking of a large commercial quantity of drugs, while a 52-year-old Epping man has been charged with cultivation.