The ministry said on Friday the number of refugees had exceeded 17,000.
"As of 11:00 [09:00 GMT], some 20,737 migrants have entered the Republic of Croatia [since the beginning of the refugee crisis]. The influx of migrants is still registering near Tovarnik checkpoint, where over 2,500 people are staying at the moment," the ministry said in a statement published on its website.
Large number of refugees have started to enter Croatia from Serbia since Wednesday, following Budapest's decision to tighten its border control with Serbia. Hungary has been so far the main transit country on the way of migrants from the Middle East to Western and Northern Europe.
Earlier on Friday, Croatian Prime Minister Zoran Milanovic stated that the country was no longer capable of registering and hosting all the refugees arriving there, and therefore had decided to start sending them to its external borders by bus.
Hungarian Foreign Minister Peter Szijjarto has condemned Croatia for inciting refugees to break a law by illegally crossing the Hungarian border.
