The last official police figure from Wednesday evening was around 1,500 people.
Croatia police say the number is much higher, pegging at around 5,650.
Croatia`s Interior Minister said that new measures might be considered the number of migrants grows.
"Croatian police have full control on the border, but if the migrants continue flowing in from Serbia in large numbers, we will have to consider other ways of handling the situation," Ranko Ostojic said during a visit to eastern Croatia late on Wednesday.
He did not specify, but he said the European Union would have to handle "hot spots" before the migrants reach Croatia.
Croatia said it could cope with several thousand people, but not with tens of thousands. The migrants are at the moment being transported to reception centres near the capital Zagreb.
Prime Minister Zoran Milanovic is scheduled to meet his Austrian counterpart Werner Faymann on Thursday to discuss the issue of migrants.
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