Some 600 police officers escorted the migrants to coaches to take them to reception centres in the Paris area.
The move comes a day after the government unveiled a series of measures to curb immigration.
Many of the migrants, who included families with children, are from Afghanistan or sub-Saharan Africa.
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The operation began in pouring rain at around 06:00 (05:00 GMT) near the Porte de la Chapelle.
The two makeshift camps, made up of tarpaulin shelters and tents, were located under the flyovers of the Boulevard Périphérique, the ring road that runs around the capital.
They are among a number of camps to emerge around the city in the last few years.
Awa, a 32-year-old woman from the Ivory Coast, said she had been sleeping in a tent at Porte de la Chapelle since she arrived in France a year ago.
"It's raining, it's cold. I don't know where I will go, but I'm glad to go because I will have a roof over my head tonight," she told AFP news agency.
On Wednesday, Interior Minister Christophe Castaner said 16,000 places would be made available in three new migrant centres, in an effort to prevent migrants from setting up new settlements.
He also said each individual case would be looked at, with more support for asylum seekers whose cases were approved and deportation for those denied permission to stay, Le Figaro reports.
France is one of many European countries to struggle with its response to an influx of irregular migrants and the government is under pressure to react to the political challenge from the far-right National Rally of Marine Le Pen.
Several European countries have tightened their migrant policies in response to the influx into the EU, which reached a peak in 2015.
On Wednesday, France said it would impose quotas on the number of foreign workers from outside the EU as part of measures aimed at addressing concerns about immigration, asylum and integration.
The move was a way to "take back control of our migration policy", Prime Minister Edouard Philippe said.
Other measures included restricted access to medical care for those who have no right to stay and the government also said migrant tent camps in north-eastern Paris would be cleared by the end of the year.