Deputy Foreign Minister Jaroslav Chlebo has said a Hungarian law on Hungarians living in neighbouring countries interferes with Slovak legislation and could hurt relations between the two states.
The law offers ethnic Hungarians living in Slovakia some educational and cultural advantages which can be claimed in Hungary.
While Budapest says the law represents no interference in Slovak domestic affairs, Bratislava maintains the opposite.
But Chlebo said Slovakia has no intention of allowing the current dispute to derail strong ties between the two states.