The centres will be located in the towns of Troisvaux and Bailleul, situated about 80 kilometres from Calais, Interior Minister Gerard Collomb said.
Interior minister's announcement came hours after France's highest administrative court ordered the state to provide running water and sanitation for the migrants, saying that its refusal so far to do so "exposed them to inhuman and degrading treatment."
The Council of State or Conseil d'Etat, which estimates the number of migrants at 400-700, was ruling on an appeal by the interior ministry and the city of Calais against an injunction issued by a court in Lille last month.
In its decision Monday the Council of State upheld the order sought by a group of charities, saying that migrants were developing skin diseases such as scabies and festering wounds as they had no way of washing themselves or their clothes.
Calais Mayor Natacha Bouchart, from the Republicans party, said she would ignore the order.
"In the absence of a national and European policy offering a global solution on controlling immigration, Calais will not implement the injunctions," she declared, warning of the emergence of "yet another Jungle" -- the sprawling informal camp from which over 6,000 migrants were evacuated last year.
Collomb however said the migrants would quickly be given improved access to water.
The minister had previously argued, like Bouchart, that the provision of services could have a pull effect on migrants who trek across Europe to Calais in the hope of stowing away on a truck crossing the Channel to England.
In June, he warned the city risked developing a migrant "abscess".
But in recent days the government has softened its tone.
President Emmanuel Macron last week promised to find temporary shelter for all those on the streets by the end of the year.
- with AFP