"We stay true to our word in Croatia and will fulfil our obligations, we shall accept those 476 refugees from the Turkish territory, but the biggest challenge will be to get these people to remain in Croatia. They will want to move on – to Germany, Austria, Slovenia or the Netherlands," Kovac said as quoted by the ministry on Tuesday.
The Turkey-EU deal has been criticized by refugee agencies and human rights campaigners, who have questioned whether Turkey can be considered a safe country for refugees.
Last year saw over 1.8 million border crossings into Europe in what has become known as the worst refugee crisis since World War II. The crisis sparked an outcry among eastern EU member state leaders over the failure of the Schengen open border systems to curb the migrant numbers.