The operation began at dawn at a camp along the Canal St Martin northeast of the city centre where an estimated 550 mainly Afghan migrants were staying.
Another 450 people were being evacuated from a camp to the north at Porte de la Chapelle, police and city authorities said in a joint statement.
The St Martin Canal is near the site of a sprawling former camp by the Stalingrad Metro stop, which was cleared only to spring up again several times last year.
Claims for refugee status will be given a "complete and in-depth examination", the statement said.
Monday's operation comes less than a week after the dismantling of a camp along the Canal St Denis, north of the St Martin canal, where around 1,000 migrants mainly from Eritrea and Sudan had sheltered.
Concerns had grown in recent weeks over the conditions at the makeshift camps. One migrant drowned in the St Martin canal last month, while a brawl left a migrant seriously injured at the St Denis camp.
"They say we can stay in shelters for not very long, that we'll have three meals a day. That's good," said a migrant who gave his name only as Souleimane, wearing a rasta cap over his dreadlocks. "Life here was very, very difficult."
Many migrants hope for refugee status but may be facing expulsion under centrist President Emmanuel Macron's tougher approach to immigration.
Some have arrived in Paris from the northern port of Calais, where migrants have flocked for years hoping to stow away on trucks to Britain.
France received a record 100,000 asylum applications last year and offered refugee status to around 30,000 people, official figures show. Forced expulsions numbered 14,900.