The barbed wire that has encroached on Croatia's territory at some sites has prompted Croatia's foreign ministry to forward several protest notes to the Slovenian authorities so far.
Slovenia must be aware that it is responsible for the damage it is doing to the people in the border area by denying them their rights, the statement said.
The note forwarded to Slovenia's embassy in Zagreb reiterates Croatia's demand that the razor-wire fence on Croatia's territory must be removed without delay.
Speaking of border fences in general, Cerar said: "No one wants a wire fence for a longer time, but right now it is necessary to control illegal migrations.
In its reply, the Slovenian government reiterated its position made known after earlier warnings to remove the fence from locations that were on Croatian territory.
By fencing off the two border crossings Slovenia has violated the 1997 Agreement on Local Border Traffic and Cooperation and it has brought into question the purpose of that agreement,
Slovenian authorities have continued putting a barbed wire fence on the country's border with Croatia in order to direct the refugee influx
Slovenia's media have reported that Austria has started erecting a 3.7-kilometre wire fence along the Spielfeld-Sentilj border crossing between Austria and Slovenia.
"Slovenia is putting up technical barriers on its territory, the border has not been defined yet and we do not know how it runs, that will be known when the arbitral tribunal makes a ruling,"
"Migrations of such a large scale as this are a big challenge to all countries in the region and it is important that they cooperate most closely in managing migrant flows,"
"Slovenia thus violated the territory of the Republic of Croatia which even according to the official Slovenian land records does not belong to the Republic of Slovenia,"
However, some Slovenian media said on Thursday that the mention of the surge of 30,000 migrants was necessary to portray the barbed wire fence as a necessary measure.
Trucks carrying wire fencing arrived in the Slovenian village of Veliki Obrez close to the border with Croatia on Wednesday, a day after the government said it would start to put up fences