"Traffic is banned on the border crossings of Tovarnik, Ilok, Ilok 2, Principovac, Principovac 2, Batina and Erdut," the ministry said in a statement.
More than 11,000 refugees have entered Croatia from Serbia since early Wednesday, the ministry added.
The refugees began heading for Croatia after Hungary sealed its border with Serbia earlier this week, cutting off a key route into the European Union used this year by more than 200,000 refugees, many of them fleeing violence in the Middle East and Afghanistan.
Croatia had said it would let people pass through freely on their way to other European Union countries —- but Prime Minister Zoran Milanovic warned his country's resources for dealing with the influx were "limited."
"We will not and cannot keep them in Croatia and no one will make us do that," he said.
Meanwhile, Slovenia announced late Thursday that it had stopped a train from Croatia carrying refugees, saying some 150 passengers would be returned to Zagreb because they did not have the necessary documents for onward travel.
Slovenia later suspended all train traffic between Slovenia and Croatia until Friday morning, Slovenian news agency STA reported.
Croatia’s statement amounted to a policy reversal a day after leaders promised to welcome refugees, a position in marked contrast to that of Hungary.
Croatia’s decision to close roads crossing into Serbia could force refugees to travel across the countryside in an area still strewn with land mines laid in the Balkan wars of the 1990s, according to The Washington Post.
Interior Minister Ranko Ostojic said earlier on Thursday that Croatia would close its border with Serbia if the inflow of refugees again hits 8,000 people a day. He also said that Croatia had no capacity to receive new refugees.
Ostojic said on Thursday that the refugees entering the town of Tovarnik from Serbia would have to seek asylum in Croatia after the authorities provided safe passage to reception centers around the capital Zagreb.
On Thursday, hundreds of refugees pushed through Croatian police lines in Tovarnik with people trampling and falling on each other amid the chaos.
The route through Croatia had represented a longer and more arduous route into Europe for the asylum-seekers from Syria and Africa fleeing violence in their homelands. But they have little choice after Hungary sealed off its southern border with Serbia on Tuesday and began arresting anyone caught trying to enter the country illegally.
The refugees in Croatia are unlikely to stay long. Most plan to travel on, passing through Slovenia and then Austria en route to Germany or the Scandinavian countries. Croatian Foreign Minister Vesna Pusic said the country "cannot force anyone to stay."