The centres will be located in the towns of Troisvaux and Bailleul, situated about 80 kilometres (50 miles) inland from Calais, Interior Minister Gerard Collomb said.
Each will have a capacity of 300, he told reporters, estimating the number of migrants currently in the northern port at 350-400.
His 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, 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.
The situation was causing "serious psychological problems", it added, calling the state's failure to address the situation "a serious and clearly illegal blow to a basic right".
Calais Mayor Natacha Bouchart, from the centre-right 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".
'Individual excesses'
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.
Collomb said the addition of two new shelters to some 450 already in operation around the country would help speed up the processing of asylum claims from those migrants who wished to stay in France.
"We do not want to repeat the bad experiences of the past," he warned, alluding to the squalid Jungle.
Collomb also announced an internal police investigation into claims of excessive force being used by officers against the migrants in Calais.
In a report entitled "Like living in hell" Human Rights Watch last week accused the police of routinely using pepper spray on asylum seekers and migrants.
Collomb said the security forces did not use pepper spray but he did not rule out "excesses by a few individuals".
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