Detectives raided the former Isle of Dogs police precinct on Sunday.
The building in Manchester Road was still cordoned off by officers on Monday as they reportedly confiscated hundreds of illegal plants.
The Met sold the building at the end of February. However, Land Registry records still show it as belonging to the Mayor's Office for Policing and Crime and do not list the new owner.
Isle of Dogs councillor Peter Golds told the Standard: "Two years ago we found a cannabis factory in a school in the borough and now this.
"We have said for years there are problems with antisocial behaviour in Tower Hamlets, but we have continued to see police stations close down.
“We only have one proper station in Bethnal Green left. "
A Met police spokesman said the force launched the raid on Sunday after it was “alerted to a potential Cannabis Factory”.
“On arrival a large cannabis factory was found which is currently a crime scene with officers at the location,” the spokesman said.
“There has been no arrest and the investigation is ongoing.
“The Isle of Dogs police station was sold to a private company on February 25, 2022 and is no longer MPS property.”
It follows a cannabis factory being discovered at the old Edgware Police Station in Harrow earlier this year.
More than 200 plants were removed from the building in Whitchurch Lane in April.
Around 100 stations closed in London between 2012 and 2017.
The force has made more than £1billion selling off assets during a massive cost cutting mission by the Mayor's Office for Policing And Crime (MOPAC).