The club is one of several late-night venues across Melbourne facing sanctions over alleged breaches of their liquor licences.

Nightclubs in South Yarra, Prahran and Windsor also face penalties, including hefty fines and a reduction in trading hours after a recent spate of drug overdoses.

Victoria Police investigated several Chapel Street venues over the weekend as part of an ongoing investigation.

South Yarra nightclub Circus faces serious penalties from police and liquor-licensing authorities after several patrons suffered non-fatal overdoses at the venue on January 14.

One of the victims is understood to have been a 17-year-old girl, who was admitted to The Alfred hospital in a serious condition after attending the club on Commercial Road.

At least three people died over the same weekend from a toxic batch of drugs sold as MDMA, which was tainted with a powerful synthetic hallucinogen NBOMe.

Five patrons are also believed to have overdosed at Chapel Street club, Revolver Upstairs, but the venue could escape punishment, after assisting police by identifying a man who was later charged with trafficking MDMA and possessing the proceeds of crime.

At the time, management of Revolver Upstairs also issued a warning to patrons on its Facebook page.

"These drugs can cause violent reactions, severe hallucinations and may result in death ??? do not risk your life with these drugs."

The club's owner is understood to have been spoken to by an inspector from Stonnington Police last month regarding the overdoses.

A police spokesman confirmed that "some venues" had been issued with penalties, but would not make any further comment because the investigation was ongoing.

A spokeswoman for the Victorian Commission for Gambling and Liquor Regulation also declined to comment on an active investigation.

Fairfax Media understands Kittens nightclub in South Melbourne, which was embroiled in a string of drive-by shootings and fire-bombings, also faces significant penalties over allegations it employed a 16-year-old girl in its cloak room.

The girl, who cannot be identified for legal reasons, was in the care of the Department of Health and Human Services when she was briefly employed by the strip club.

Kittens owner Jason Dimozantos did not respond to calls from Fairfax Media on Sunday.

The venue has been a major source of problems for police, who have investigated a vicious battle between the Comanchero outlaw motorcycle gang and several venues owned by Mr Dimozantos, following a dispute with the security firm employed at his venue.

In August 2016, it was revealed Mr Dimozantos had attempted to negotiate a secret financial settlement with the Comanchero gang in a bid to resolve the violent two-year feud.

There have been no further attacks on the club since the report.