Heger, who was leading an interim government after his own four-party coalition collapsed in December last year, submitted his resignation to President Zuzana Caputova.
"I have asked the president to revoke my mandate," Anadolu Agency quoted Heger as saying.
Heger said he will leave it to the president to try to bring Slovakia to free and democratic elections with an interim government.
Earlier this week, Heger's Agriculture Minister Samuel Vlcan decided to step down, a move followed by Foreign Minister Rastislav Kacer's resignation.
Meanwhile, Caputova reportedly confirmed that a technical government will be appointed on May 15.
MP/PR