Rupel was taking part in a meeting of European Union foreign ministers, where he held talks with several of his colleagues on incidents near the border crossing Sveti Martin na Muri-Hotiza on the Croatian-Slovene border.
"I spoke with some of my colleagues and was glad to inform them of the agreement. The critical point has been overcome," Rupel said.
The agreement on the reconstruction of the dyke on the River Mura was signed on Thursday evening in Otocec ob Krki by the Croatian and Slovene co-chairmen of the joint commission on water management, Zdravko Krmek and Marko Starman.
Early on Friday morning Slovene special police units withdrew from the border near the Sveti Martin na Muri-Hotiza border crossing, after which Croatian police withdrew as well.
Rupel said that he discussed the issue also with the EU High Representative for the Common Foreign and Security Policy, Javier Solana, and Enlargement Commissioner Olli Rehn.
Rupel said he would discuss the issue with his Croatian counterpart Kolinda Grabar Kitarovic and EU High Representative Solana on the margins of a session of the UN General Assembly in New York next week.