The man's fate and when the video was taken were unclear. The footage shows him screaming on the floor in a fetal position with his genitals bound and a man pulling the rope and whipping him.
"Snatching is not allowed here," the man beating the detainee was heard as saying, while a uniformed officer stood by and watched.
Metropolitan Manila police chief Leocadio Santiago relieved the 11-member police station Wednesday and ordered its commander, Senior Inspector Joselito Binayug, investigated for criminal acts.
Maximum penalty under an anti-torture law passed last year is 40 years in prison if the victim dies.
"We are holding Binayug responsible. We will be filing charges for dereliction of duty but we want something heavier," Santiago told reporters.
Binayug could not be reached for comment as the precinct does not have a working phone and the chief did not provide his phone number.
It is not clear if the 10 others will also face charges, but that will be part of the investigation, police said. New officers were assigned to the precinct under investigation.
President Benigno Aquino III said torture is not a government policy. Asked about the incident at a news conference, Aquino said "the police also are entitled to their day in court and to due process."
Coco Quisumbing, an official of the Commission on Human Rights, which said it would separately investigate the torture allegations, said she was aghast after seeing police officers in the video seemingly showing indifference.
Amnesty International researcher Hazel Galang said the incident can serve as a test case for the country's anti-torture law and the Aquino government's determination to implement it.
"Tomorrow is the 50th day of the Aquino presidency and in the first 50 days we've already seen torture cases, we've seen extrajudicial killings," she said. "We will keep on watching."
It was not the first time that video footage allegedly of police torture has surfaced in the country. Early this year, a police colonel was seen punching a suspect whose face was covered with a plastic bag, and recently, another video showed three handcuffed teenage boys, two of them forced to kiss each other.
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The colonel in the video was relieved and placed under investigation while the probe into the other case was incomplete because there were no witnesses and the boys did not file a complaint, police said.