Two former Serbian spy chiefs in Slobodan Milosevic's regime were convicted of war crimes Wednesday in the last and longest-running trial at the UN tribunal for the 1990s Balkans conflict.

Judges sentenced Jovica Stanisic, the ex-head of Serbia's state security service, and his deputy Franko Simatovic to 12 years in jail for backing a Serb death squad that terrorised a Bosnian town in 1992.

But the Hague court said there was not enough evidence to support allegations that Stanisic, 70, and Simatovic, 71, were responsible for wider atrocities across Bosnia and Croatia.

The conviction followed a years-long retrial after the pair were initially acquitted in 2013, and marks the tribunal's final case from the wars that tore apart Yugoslavia after the fall of communism.

Chief Judge Burton Hall said the court "finds Jovica Stanisic and Franko Simatovic guilty" of the war crime of murder, and the crimes against humanity of murder, persecution, forcible transfer and deportation.

Munira Subasic, president of one of the "Mothers of Srebrenica" associations that campaigns for justice for victims of the 1995 massacre of some 8,000 Muslim men and boys, told AFP that "this judgement will do justice to the victims of Bosnia."

Serbia's former secret police chief Jovica Stanisic is accused of backing paramilitary groups behind a reign of terror in Bosnia and Croatia
Serbia's former secret police chief Jovica Stanisic is accused of backing paramilitary groups behind a reign of terror in Bosnia and Croatia AFP / Martijn Beekman

Judges said the pair helped train and deploy Serb forces during the takeover of the town of Bosanski Samac in April 1992, "which had a substantial effect on the commission of the crimes", the court said.

Serb forces launched a "campaign of terror" to drive out non-Serbs involving rapes, looting and the destruction of religious buildings in the town, as well as holding Bosnian Muslims and Croats in six detention centres, the court said.

"Detainees were kept in inhumane conditions, and were subjected to forced labour, severe mistreatment, repeated beatings, and torture, forced to engage in sexual acts, and killed," the judgment said.

Sixteen men were killed in one specific incident in May 1992, it said.

The court said that Stanisic and Simatovic were "criminally responsible for aiding and abetting" the crimes in the town, but not for planning or ordering any other crimes.

UN prosecutors say Stanisic and Simatovic were part of a joint criminal enterprise
UN prosecutors say Stanisic and Simatovic were part of a joint criminal enterprise ANP / Michael Kooren

The judges also said there was not enough evidence to back prosecution claims that the pair were part of a joint criminal enterprise that included the late Serbian president Milosevic, who died in The Hague in 2006, to drive out Croats and Bosnian Muslims and create a Serb homeland.

The prosecution argued the two men had backed notorious paramilitary groups including an elite Serbian unit dubbed the "Red Berets" and the feared "Tigers" outfit run by Zeljko "Arkan" Raznatovic.

UN prosecutor Serge Brammertz said the convictions were "steps forward" but that his office would help national courts bring other suspects to justice.

"While this is the last trial held in The Hague, there remain thousands of war crimes suspects throughout the countries of the former Yugoslavia who remain to be prosecuted," Brammertz said in a statement.

Stanisic's defence lawyer Wayne Jordash said they would appeal "for sure".

"It looks like a cynical compromise, that they have to find some way to convict him, to justify why they put a man on trial for 18 years," he said.

"It's the longest trial in international criminal law, if this was an authoritarian regime people would be horrified."

While Simatovic could be released immediately because of the amount of time he has already served behind bars, Stanisic could still have "quite a stretch" left, he added.

Stanisic and Simatovic were arrested in 2003 and their first trial began in 2008. After their shock acquittal in 2013 the court ordered a retrial in 2015, saying the original judges had made legal errors about the pair's criminal responsibility.

Wednesday's verdict was welcomed in the region even if it did not draw much attention.

"The fact that the Serbian security chief and Milosevic's right-hand man has been convicted of war crimes in Bosnia-Herzegovina is of historic significance," said Sefik Dzaferovic, the Muslim member of Bosnia's tripartite presidency.

The Balkans wars left some 130,000 people dead and millions displaced.