Two men who manage a Melbourne pub have appeared in court and been remanded in custody on drug trafficking charges after a large quantity of drugs were allegedly seized during recent police raids.

Fairfax Media revealed on Thursday that drug taskforce detectives allegedly found thousands of ecstasy pills, methamphetamine and cash during separate raids at Brunswick's Railway Hotel and Melbourne nightclub Two Floors Up.

The Railway Hotel in Brunswick. Credit:Jason South

Paul Polito, 37, the manager of the Railway Hotel, appeared via video link before Melbourne Magistrates Court on Thursday, on charges of trafficking ecstasy, amphetamines and cocaine.

Chris Lytras, 47, believed to own the hotel, separately appeared before a magistrate on similar charges.