Lawmakers voted 129 to 1 to repeal the amnesty offered in 1998 by prime minister Vladimir Meciar for "crimes committed in connection with the kidnapping of Michal Kovac Jr".
The son of president Michal Kovac was seized in August 1995 by unknown assailants in neighbouring Austria.
He was blindfolded and handcuffed, forced to drink a bottle of whisky and given electric shocks, before he was found in his car near a police station in the Austrian town of Hainburg, just 15 kilometres (nine miles) from Bratislava.
An Austrian court ruled in 1995 that the kidnapping was most likely the work of the Slovak Secret Service (SIS).
But Meciar's amnesty a few years later halted investigations, heightening widespread suspicions that he himself orchestrated the abduction to embarrass Kovac, his main political rival.
Meciar, now 74, has denied any involvement, but a recent opinion poll showed that 63 percent of Slovaks still want to see the kidnapping investigated.
"The amnesty overturned today was unprecedented in postwar Europe, as a state representative de facto amnestied perpetrators of state terrorism -- and it is suspected that he (Meciar) also amnestied himself," Jan Baranek, an analyst with the Polis Slovakia think tank, told AFP.
But Baranek said any new inquiry would be difficult, not least because Ivan Lexa, the SIS director at the time, now lives in Mexico, "a country with which we have no extradition treaty".
Meciar, who served three times as prime minister, was sharply criticised by the United States and many European nations for his authoritarian rule and widespread corruption while in office.
He was also condemned by Kovac, the first president of an independent Slovakia, for attempting to curb newly won civil liberties after the collapse of communism in 1989.
Kovac died of heart failure in October 2016.
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