Officials said they had no choice after more than 13,000 people entered the country since Hungary fenced off its border with Serbia earlier this week.
Many have been taken by bus to reception centres but some say they plan to walk to neighbouring Slovenia.
Huge numbers of people heading north from the Mediterranean have created a political crisis in the European Union.
Croatian officials said roads leading to the border crossings had also been shut.
The crossing on the main road linking Belgrade and Zagreb – at Bajakovo – appeared to be the only one left open.
Local media reported severe congestion at the crossing, with a 6km queue of lorries back into Serbia.
On Thursday, Croatian Interior Minister Ranko Ostojic said his country was “absolutely full”.
He said his message to the migrants was: “Don’t come here any more. Stay in refugee centres in Serbia and Macedonia and Greece. This is not the road to Europe. Buses can’t take you there. It’s a lie.”
But a Reuters journalist at the scene reported that migrants were walking through fields to bypass one of the border crossings.
Scuffles broke out in two locations on the border with Serbia on Thursday after people were left waiting for hours for transport further north.
Crowds briefly broke through police lines at Tovarnik and Batina – two of the crossings now closed.
The BBC’s Lyse Doucet, at Tovarnik, said buses arrived just before midnight but not enough to transport everyone. Drivers said people were being taken to a reception centre.
But many appear to have slipped away to continue their journey north on foot.
One man, a Syrian from Homs called Hanny, told the BBC that people were walking without sleep.
“There’s no time. The rules change every day,” he said.
