"The NZS and national team coach Matjaz Kek have reached an agreement to end cooperation by mutual consent and we thank him for what he has achieved during his spell in charge," it said in a statement.
"There is no doubt that Kek did a good job and we wish him well in the future."
The 50 year-old coach, a former Slovenia defender, took over in 2007 and steered Slovenia to the 2010 World Cup finals in South Africa but failed to repeat the success in Euro 2012 qualifying.
Local media have tipped Slavisa Stojanovic, who won two Slovenian league titles with NK Domzale before becoming an assistant to Srecko Katanec at the United Arab Emirates, to take over from Kek.
Slovenia finished fourth in their Euro 2012 qualifying group behind Italy, Estonia - who clinched a play-off berth for the first time in the Baltic nation's history - and fellow former Yugoslavs Serbia.
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