An independent inquiry has called on the United Nations to investigate the "systematic and widespread" murder of political opponents by Ayatollah Khomeini's regime in Iran during the 1980s.

In its judgment at the end of a three-day session in The Hague, the Iran tribunal found that the Islamic regime had committed "gross human rights abuses" including torture, sexual violence, extra-judicial executions and unjust imprisonment.

The ruling is the culmination of a five-year co-operation between international human rights lawyers, exiled Iranians and relatives of the victims. As many as 20,000 people, mainly youths, are believed to have been killed in the state's prisons during that decade.

The first stage of hearings took place in London this summer at Amnesty International's premises. About 75 witnesses, many surviving detainees, gave evidence – some in person, others via videolink.

The final stage was held in the Peace Palace, home to the UN's international court of justice in The Hague. Proceedings were broadcast live online. The Iranian government was invited to participate but declined to reply or attend.

The tribunal was based on the model developed by a private international war crimes tribunal established in 1966 by Bertrand Russell and Jean-Paul Sartre to investigate the US war record in Vietnam.

In his closing speech, the British international lawyer Sir Geoffrey Nice QC, the tribunal's prosecutor, said the graves of the executed stretched "as far as the eye can see; the gravedigger of Shiraz reported the delivery of 60 bodies on a single occasion, of victims at most 20 years old.

"Men were arrested at 10 in the morning and were dead by 11; entire families were eliminated and whole wards purged; rows of prisoners were shot by firing squad, still breathing until they were finished off by coup de grâce."

One of the most chilling accounts was given by a man who admitted that as a child he was forced to shoot any survivors in the head. Nice added: "Truckloads of bodies were tipped into mass graves … In no case was an execution ordered in accordance with due process.

"There has been not one witness who was not tortured in prison, both physically and mentally. Prisoners were hanged from the ceiling by their arms, flogged on the soles of their feet, beaten, deprived of sleep, kept in solitary confinement, subjected to mock executions and forced to watch other prisoners being tortured – or were tortured in the presence of their children.

"Shokufeh Sakhi told the tribunal how she was subjected to sensory deprivation in a dark box (the 'coffin') for hours on end, month after month. The general effect was to turn prisoners into zombies by destroying their senses of self and dignity.

"Another witness told the tribunal of the psychological rape that turned him into a puppet, who would shoot his fellow prisoners as member of a firing squad of tavabeen (repenters)."

Prisoners' families were forced to pay for the bullets used to shoot their loved ones and assaulted when they tried to hold mourning services, the tribunal heard. Gravestones were smashed; mothers were refused the right to recover their children's bodies.

In its judgment, the Iran tribunal found that the Islamic Republic of Iran bears absolute responsibility for gross violations of human rights against its citizens and "crimes against humanity under customary international law as applicable to Iran in the 1980s".

Among its recommendations, the tribunal called on the human rights council of the United Nations to establish a commission of inquiry to investigate "these atrocities".

The tribunal was composed of six judges including the UK barrister Michael Mansfield QC, John Dugard, a South African professor of international law, and Professor Patricia Sellers, a former UN adviser on human rights.