Slovenian soldiers removed 200-300 metres of the fence in the Griblje and Dragatus areas, villages some 110 kilometres (70 miles) south of Ljubljana, after the Kolpa burst its banks and floodwaters threatened to tear down the fence, the STA news agency reported.
Since mid-November Slovenia has built over 150 kilometres of razor-wire fence along its border with Croatia, hoping to prevent an uncontrolled inflow of migrants across the "green border".
The Slovenian government's information office said Monday that the border fence would be removed in areas where the stream of the Kolpa river was strongest and replaced, in the near future, by a more resistant fence.
Situated in one of Slovenia's most attractive natural parks, the Kolpa river marks over 100 kilometres of the 670 kilometre-long Slovenia-Croatia border.
The fence has been criticised by environmentalists and civil groups in Slovenia and Croatia which claim the razor wire is a threat to wildlife.