Justices S. Muralidhar and Vinod Goel reversed a 2005 judgment of the trial court, which had acquitted the 16 men on charges of murder and other crimes, and held them responsible for criminal conspiracy, kidnapping, murder and disappearance of evidence.
The High Court was hearing pleas challenging the trial court decision.
"The present case is yet another instance of custodial killing where the legal system has been unable to effectively prosecute the perpetrators of gross human rights abuses," the court said.
"The prolongation of the trial for over two decades, compounded by the endemic systemic delays, have frustrated the attempts at securing effective justice for the victims."
The High Court held that this amounted to targeted killings by an armed force "of the unarmed, innocent and defenceless members of a particular community" and called it a disturbing aspect of the case.
There were originally 19 accused but three died during the prolonged trial. All the 16 from the PAC are now retired.
The High Court directed the convicts to surrender on or before November 22. If they failed, then the concerned Station House Officer (SHO) were ordered to take them into custody.
Vibhuti Narain Rai, the then Superintendent of Police in Ghaziabad who registered the first FIR in the case on the night of May 22-23, 1987, told IANS: "This was the first and biggest custodial massacre in independent India.
"There was a similar carnage in Nellie (Assam) but that was not in police custody unlike this."
The Hashimpura victims, all Muslims, were picked up from the Hashimpura neighbourhood by the 41st Battalion of the PAC during a search operation, taken away in trucks, lined up and shot dead in cold blood. The bodies were dumped in a canal.
The men shot at were said to be 42 but four of them escaped by pretending to be dead.
The charge sheet was filed before the Chief Judicial Magistrate in Ghaziabad in 1996.
The case was transferred to Delhi in September 2002 on the Supreme Court's orders following a petition by the families of the victims and the survivors.
A sessions court here in July 2006 framed charges of murder, attempt to murder, tampering with evidence and conspiracy against all the accused.
The Delhi High Court said: "...the relatives of the victims who died as a result of the brutal and bone-chilling action of the PAC remained in the dark about not only the fate of the victims themselves but also about the steps taken to investigate the case and unearth the truth.
"Indeed, their 31 years of waiting for justice may have eroded their faith in the state machinery.
"This case involves the killing of around 38 innocent persons in cold blood by members of an armed force, the PAC. The gravity of the crime is obvious.
"We are conscious that for the families of those killed, this (punishment) is perhaps too little, too late," the court said, adding that they were reversing the acquittal by the trial court of the accused.
Observing that compensation they have received cannot make up for the lives lost, the court recommended state legal services authority to address the needs of the victim families in the case of custodial killings or state excesses.
The killings took place amid communal riots in Meerut.
Former police officer Rai, who later brought out an investigative book on the massacre, recalled that it was one and a half hours after the killings that they got to know about the mass killings by the PAC.
"We could rescue one person, Babudin. It was on his description of the massacre that we registered the FIR."
He said the Muslim youngsters were randomly picked up from the Hashimpura locality, taken through Ghaziabad and thrown into water canals after being indiscriminately shot at.
"It was a chilling, shocking massacre. Before I could launch my investigation, the case was handed over to the Crime Branch of the CID," said Rai, who retired as Director General of the Uttar Pradesh Police (Vigilance) and later served as Vice Chancellor of the Mahatma Gandhi Hindi Vishwavidyalaya at Wardha.
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