The police unit responsible for investigating criminal offenses related to terrorism is the Counterterrorism Unit (CTU) of the Bureau for Combating Organized Crime. The CTU develops Slovakia's counterterrorism strategy, conducts criminal investigations, and makes arrests of suspected terrorists or extremists within Slovakia's borders. Slovakia's most recent strategy, approved in October 2007, focuses on developing the legislative and institutional framework to combat terrorism, as well as strengthening coordination, collaboration, and exchange of information among key institutional actors. The Financial Intelligence Unit (FIU) of the Bureau for Combating Organized Crime and the Slovak Information Service (SIS) provides support to CTU's counterterrorism mission. On December 16, President Ivan Gasparovic signed a law making the financing of terrorism a punishable criminal offense in Slovakia. According to the amended Penal Code, financing terrorism can be punished by 20 to 25 years imprisonment.

One suspected terrorist, Mustapha Labsi, has been held in Slovak custody since May 2007. In January 2008, the Supreme Court confirmed that he could be extradited to Algeria, where he was convicted in absentia to life in prison. In June, the Constitutional Court ruled that the Supreme Court must verify that Labsi will not face torture upon extradition. On October 28, the Regional Court in Bratislava decided again not to grant asylum to Labsi due to the serious threat he could pose to the security of Slovakia. On December 19, Labsi left a refugee detention center and fled to Austria, where he was apprehended by police. Labsi had not been returned to Slovakia at year's end.

Slovakia cooperated closely with a range of international partners in numerous fora. Slovak police participated in the Police Working Group on Terrorism, a consortium of 30 countries, including EU member states, Norway, Switzerland, Iceland, and Croatia. The SIS is engaged in the Club de Berne, which facilitates exchange of police and intelligence information on terrorism. Both CTU and SIS take a part in the EU's Joint Situation Center.

In August, Slovakia hosted a conference on "Legal Aspects of Combating Terrorism and handling extremism" under the auspices of the U.S. Office of Defense Cooperation-U.S. Embassy. A result of the conference was the creation of a forum for discussion between nine countries, the SIS, and the ministries of Defense, Interior, Justice, and Foreign Affairs.

In 2009, Slovakia increased its presence in Afghanistan from 51 soldiers to 319. This includes a substantial contingent in Uruzgan province, a very active operational area, as well as in Kandahar.

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