Croatian police said on Thursday that 5,650 migrants had entered Croatia so far.
The migrants from the Middle East have changed their Balkan route on Wednesday after Hungary closed its border with Serbia and they turned westwards into Croatia.
"The migrants can be seen entering Croatia around several crossing points," police said.
Croatia is transporting the migrants to reception centres around the capital Zagreb after registering them. It said it could cope with several thousand migrants, but not tens of thousands.