A Macedonian police statement said 42 migrants were Pakistani, two Afghans and one Syrian. They were seen leaving the van near the border.
The migrants are believed to have entered the country illegally from Greece and paid the smugglers to send them to Serbia, then cross the border to reach any European Union country. Police said the men were taken to a camp in Gevgelija, awaiting deportation to Greece.
Police officials have also said they have detained 10,017 migrants who have entered the country illegally in the first half of this year.