The government's human rights commission discovered a dozen men and women packed into the tiny cell behind a wooden cabinet during an unannounced visit to a police station in a Manila slum neighbourhood on Thursday.
The resulting outcry saw officers suspended and an official inquiry launched, but on late Friday national police chief Ronald Dela Rosa visited the police station and defended his men's actions.
"As long as the prisoners were not tortured or extorted, it's okay with me," he told reporters.
The detainees have since been moved to a regular prison cell.
They had told the rights commission they had been held for about a week after being arrested on allegations of drug use or trafficking and that police had demanded hefty payments in exchange for their freedom.
Dela Rosa rejected the allegations and accused the rights commission, an independent government body, of plotting to embarrass Duterte's government.
The commission's spokeswoman Jacqueline Ann de Guia denied the prison visit had been organised deliberately to coincide with the Association of Southeast Asian Nations summit, which Duterte was hosting Saturday.
"The (commission) cannot sit idly nor ignore any information which may involve a serious human rights violation," de Guia told AFP in a text message, adding the government body was "impartial and non-partisan".
Manila police chief Oscar Albayalde has conceded that congested detention facilities are widespread.
Duterte won last year's presidential election on a pledge to kill tens of thousands of criminals.
Police have since reported killing 2,724 people as part of Duterte's anti-drug campaign, although authorities insist the shootings have been in self defence.
Many thousands of others have been killed by shadowy vigilantes, according to rights groups.
Duterte briefly suspended all police from the crackdown in January after an official investigation found drug officers kidnapped a South Korean businessman and murdered him as part of an extortion scam.
At the time, Duterte described the police force as "corrupt to the core" and vowed it would not be allowed to prosecute the drug war until its ranks had been "cleansed".
But he redeployed police onto the drug war about a month later, without major reforms.
International rights monitor Human Rights Watch on Saturday called on the Philippines to free all "unlawfully detained" suspects and abolish unofficial police lock-up cells.
"Secret jails may just be one more form of police criminality that has multiplied during the drug war," the group's deputy Asia director Phelim Kine said in a statement.
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