Police said they shot and killed Carl Angelo Arnaiz, 19, as he robbed a taxi driver with a handgun in northern Manila on August 17.
The young man's parents dispute the police account. On Monday the justice ministry ordered an official investigation, said Justice Secretary Vitaliano Aguirre.
"The autopsy result appears contrary to the police allegation that he (Arnaiz) had allegedly fought back," Aguirre told reporters.
Tortured
A forensic examination by a government agency which provides legal services to the poor found that Arnaiz was tortured and shot dead while handcuffed.
"He was beaten up, his body was full of welts, he had a black eye, gashes, as well as handcuff marks," Public Attorney's Office chief pathologist Erwin Erfe told reporters, adding that bullet trajectories suggested Arnaiz was shot while kneeling.
Arnaiz was killed the night after local police allegedly murdered 17-year-old Kian Delos Santos, in the same district during a major anti-drug raid on August 16.
Justice ministry investigators last week recommended murder charges against four Manila police officers. The National Bureau of Investigation (NBI) found they intentionally killed Delos Santos and fabricated evidence against him.
Street protests
Delos Santos' killing led to rare street protests against Duterte's war on drugs. Police have killed more than 3,800 drug suspects since he began his presidency in July last year.
Thousands of others have died in unexplained circumstances over the same period.
Disappearance
Rights groups have expressed alarm at what they say are a wave of extrajudicial murders, a claim the Duterte government rejects.
Persida Acosta, head of the Public Attorneys' Office, told reporters that Arnaiz and a 14-year-old neighbour who remains missing had disappeared from their homes in an eastern Manila suburb 10 days before Arnaiz's remains ended up in the morgue.
Arnaiz had dropped out of the country's most prestigious university because he had become depressed over the absence of his mother, who worked in the Middle East, Acosta added.
Justice Secretary Aguirre said he had ordered the NBI to locate the missing 14-year-old boy.
