Photograph: HINA / Željko DRAŽENOVIĆ / mm

The Croatian Ministry of the Interior on Thursday denied reports by the Slovenian media and accusations by the Slovenian authorities that the Croatian police were allowing migrants to wade through "the cold Sutla river" to get into Slovenia and were treating them inhumanely.

Right at the start of the wave of migrants, who are fleeing war and poverty in the Middle East, Asia and Africa, Croatia offered Slovenia cooperation and assistance in the form of a train that would transport migrants straight to Sentilj on the Slovenia-Austria border, the ministry said.

"Slovenia rejected the proposal, and the fact that Slovenia takes in too small a number of migrants at official border crossings has resulted in migrants seeking other ways to cross into Slovenia," the Croatian Ministry of the Interior said in a statement posted on its website.

"This way of crossing the border is unsafe for the migrants and the Croatian police did not encourage it in any way nor will they encourage it. This is exactly why Croatia has decided to organise transport through its territory by train and by bus. A new train has been notified to Slovenia and the press are invited to cover the disembarkation and reception of the migrants," the statement said.

The Croatian ministry denied reports that more than 12,000 migrants had entered Slovenia from Croatia on Wednesday. It called on the Slovenian authorities to accept migrants "in sufficient numbers" so that they would not be put at risk.

Between midnight and 3pm on Thursday, 3,513 migrants arrived in Croatia, and 2,684 were staying at the Opatovac reception centre, eastern Croatia on Thursday afternoon. More were expected to arrive from Serbia.

Since the outbreak of the migrant crisis in Croatia in mid-September, 219,774 have entered the country, the ministry said on its website.

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