The shutdown comes after the Commission on Human Rights released a study on Monday that revealed the maltreatment that occurred at the facility.
Twelve policemen, including the head of the Laguna provincial police and the chief of the police intelligence branch, were relieved of their duties while an investigation is completed, the Philippine Daily Inquirer reported.
Chief Supt. Joselito Esquivel, the regional police director, said the station was set to be turned over to his command next month.
He took it over immediately due to the commission's report and shut the facility down.
Esquivel said the officers rented the bungalow apartment to use as cells due to jail overcrowding.
Courts were aware of the detention center, but it was not authorized by law, he said.
Twenty-six inmates at the facility were transferred to a jail next to City Hall in Barangay village, the Inquirer reported.
The commission released its report after discovering a roulette wheel that was used to determine how detainees would be tortured.
Torture choices included the 20-second "Manny Pacquiao," which meant that a detainee would be punched non-stop for 20 seconds.
Twenty-nine detainees have filed charges against the policemen.