Apostile on Slovak documents have to be arranged with institutions in Slovakia as followed: 

• Regional courts – for public documents issued by district courts, notaries, court officials or official translattors. 
• Ministry of Justice – other justice documents not mentioned in the first paragraph 
• Ministry of Interior – Official documents issued by the Ministry of Interior
• Ministry of Education – University diplomas and other Education cocuments (more info)
• Ministry of Health - Official documents issued by the Ministry of Health
• Ministry of Defense - Official documents issued by the Ministry of Defense
• Local Municipalities – Birth, Marriage and Death certificates and other documents issued by local administration.
• Ministry of Foreign and European Affairs – all other official documents issued by Slovak authorities including Criminal records, documents issued by Tax Authority, Ministry of Economy, Business chambers, Land registry, etc.

Regarding apostilation of documents issued by Israeli Authorities - more information