"We have informed the European Commission that we will temporarily depart from Schengen rules," Interior Minister Jan Jambon said in Brussels in the latest blow to Europe's 26-country borderless zone.
"We will carry out border controls at different strategic locations, at spots used by smugglers which the police have detected," he said.
He said the operation would involve 250 to 290 police officers carrying out checks around Zeebrugge and the port of Bruges, a top tourist destination.
"We want to avoid tent camps like Calais in Belgium at all costs. It's a question of maintaining order," Jambon said.
The Jungle has also played into fraught discussions about Britain's possible exit from the European Union.
Some British opponents of "Brexit" say they would lose the ability to call on France to stop the flow of refugees sneaking aboard lorries and ferries in Calais if Britain leaves the EU.
The migrants in Calais make up a tiny fraction of those fleeing war and poverty in the Middle East and Africa. They are often drawn to Britain by family or community ties, or because of a shared language.
Many Jungle residents appeared to be standing firm.
"I don't have anywhere else to go," said John, a 28-year-old Sudanese national.
"We don't want to leave Calais because we don't want to get further away from England, which is still our goal."