A total of 1,095 migrants arrived in Croatia on Thursday morning, and 530,667 have passed through the country since mid-September on their way to western and northern Europe, the Ministry of the Interior said.
Only seven migrants stayed at the winter reception centre in Slavonski Brod, about 200 kilometres east of Zagreb.
The ministry said that 2,138 migrants had arrived in Croatia on Wednesday and that more were expected to come via Serbia.
The number of refugees and migrants arriving by land and sea in the European Union has passed one million this year, while a further 3,600 died or went missing, the UN High Commissioner for Refugees (UNHCR) and the International Organisation for Migration (IOM) said on Tuesday.
The UNHCR said it expected arrivals to continue at a similar rate in 2016, but IOM spokesman Joel Millman said it was impossible to forecast their numbers.