CRS riot police were deployed at dawn, some arriving by boat, as the migrants emerged from their tents and waited patiently to be bussed away from the Port de la Villette camp in the north-east of Paris.
Most of the people living in the makeshift camps on the edge of a canal in the Villette area come from the horn of Africa.
The migrants would be housed temporarily at more than 20 sites across the Paris region while the authorities checked their identities, Interior Minister Gérard Collomb said in a statement.
This is the 35th police operation to have taken place in the French capital since mid 2015.
Aid groups working earlier this month called on authorities to address deteriorating conditions at the camp, warning of security and health risks.
Louis Barda of medical charity Médecins du Monde (Doctors of the World) said the situation had been steadily worsening, calling the Villette camp "unlike any we've ever seen in Paris".
Tensions in the camp had seen people needing treatment "after being hit with iron bars, people with gaping wounds, knife cuts", he said.
One man drowned after falling into the canal earlier this month.
Aid groups say the camps in Paris have attracted smugglers from the port city of Calais, offering them a chance to reach Britain, where many migrants believe it would be easier to find work and potentially asylum.
Two similar camps in the capital - one along the Canal St Martin which houses 800 mostly Afghan migrants, the other at Porte de la Chapelle, home to 300-400 people - would also be quickly evacuated, said regional prefect Michel Cadot.
The camps have been the focus of a row between the city council and the government over whose responsibility it was to clear them and what facilities would be provided for the occupants.