Czech psychology students Hana Humpalova and Antonie Chrastecka, both 24 at the time, were seized by armed men in March 2013 in Pakistan's southwestern Baluchistan province, near the borders with Afghanistan and Iran.
The pair had entered from Iran as tourists and were escorted into Pakistan by a tribal policeman.
In a video released shortly after their kidnapping, the two young women had pleaded for the release of Pakistani neuroscientist Aafia Siddiqui, jailed in 2010 in the United States on charges of terrorist links.
Negotiations with the kidnappers on the payment of a ransom were carried out by the Czech state's security council, according to Respekt.
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"The talks weren't easy, but in the end, none of us wanted to assume responsibility for the death of two young girls," the weekly quoted an anonymous participant in the negotiations as saying.
"The decision to hand over the ransom was taken unanimously," the source added.
Government spokesman Martin Ayrer told AFP that Sobotka "will not be commenting on this report".
Their release appeared to be tied to the detention of a Lebanese man in Prague, with a Lebanese security official telling AFP: "The release of the five Czechs... Is the final part of an exchange deal, (that) includes the release of the Lebanese detainee in Prague, Ali Taan Fayyad.