By Paul Cunningham, Europe Correspondent

The UN court based in The Netherlands, which was established by the Security Council to consider war crimes perpetrated during the collapse of the former Yugoslavia, is facing into its most difficult year since its establishment back in 1993.

The International Criminal Tribunal for the former Yugoslavia has successfully arraigned all 161 people it was charged with judging.

Yet its independence is being called into question by three separate rulings it has delivered at the end of 2012.

Based in The Hague, and known as the ICTY, the UN court dealing with the horrors of the Yugoslav wars in the 1990s is suddenly in trouble over its interpretation of a legal phrase called “joint criminal enterprise”.

It’s clear that war crimes were perpetrated by all sides in places like Bosnia-Hercegovina – a grisly conflict I covered in 1994 and 1995.

One of the tough questions the ICTY has had to answer is whether such crimes were horrors carried out by local forces or the grim result of a cold-blooded conspiracy, involving an ethnic group’s senior political and military leadership.

That issue came to the fore in November when the ICTY quashed the convictions of two Croatian generals who led a military operation in which Croatia re-took territory held by Serb separatists for four years.

During the 1995 Operation Storm, between 150 and 200,000 Croatian Serbs fled in a matter of days. Serbia maintains they fled after their towns and villages were shelled by Croatian forces intent on forcing them from the territory.

In releasing Generals Ante Gotovina and Mladen Markac, the ICTY was interpreted as having confirmed that the Croatian leadership had not been involved in a joint criminal enterprise; they had not collectively connived in a war crime.

While it was a majority rather than a unanimous finding, the ruling triggered wild celebrations in Croatia while the reaction in Serbia was one of outrage.

Just a few days later, the ICTY made another major decision – this time regarding the 1998-1999 conflict between the Kosovo Liberation Army and Serbian forces.

Ramush Haradinaj, a KLA commander who later became Prime Minister of the breakaway region, was cleared of overseeing a campaign of torture and murder against ethnic Serbs – and others – at detention camps.

In Kosovo’s main city Pristina – crowds celebrated on hearing the verdict.

Haradinaj’s acquittal once again was interpreted that the Kosovo’s leadership had not been found to have engaged in a joint criminal enterprise.

In the Serbian capital Belgrade, there was a torrent of abuse directed at The Hague.

Then in early December, the ICTY judged that a joint criminal enterprise had happened. In a majority, rather than unanimous decision, the Court made the ruling in the trial of wartime Bosnian Serb general Zdravko Tolimir.

Sentencing him to life in prison, the bench found that Tolimir had been involved in genocide against the Bosnian Muslim populations in Srebrenica and Zepa.

Tolimir’s commander, Ratko Mladic, is currently standing trial. The Bosnian Serb political leader, Radovan Karadzic, is also on trial.

So within just two months, the Croatian and Kosovar leaderships had been found by the ICTY not to having been involved in a joint criminal enterprise, but the Bosnian Serb leadership was.

Serbia’s Deputy Prime Minister Rasim Ljajic claimed the ICTY has lost all credibility and branded The Hague as a place of ‘selective justice.’

The Serbian President Tomislav Nikolić has said that the judgment in the Kosovo case was unjust.

This criticism was levelled, even though the ICTY has convicted Croats, as well as both Bosnian Muslims and Kosovo Albanians, for crimes committed against Serbs and others.

To a certain extent, judgments in such a war were always going to result in criticism.

To its eternal credit, however, the ICTY has been a forum which has laid bare the horror of the murder, torture, rape, enslavement and destruction of property that took place in Bosnia, Croatia and Serbia.

Yet in the short-term, the ICTY faces a very tough 2013.

It’s not just that significant judgments are pending over the next 12 months, but Serbia has also moved to bring its concerns of bias to the UN General Assembly.