"This distinction, I don't understand it," Cazeneuve told France 2 television. "I condemn and it seem dreadful to me."
A number of minorities are suffering persecution in the region, Cazeneuve went on. "Eastern Christians must be taken in but there are also Muslims who are being persecuted and there are other minorities who are with the same amount of barbarism."
Some French mayors have said they only wished to accept Christians in their towns, the mayor of Roanne, central France, Yves Nicolin, arguing that the restriction would keep out "terrorists".
The mayor of Belfort, Damien Meslot, who is also an MP for the mainstream right Les Républicains, also said he was thinking of taking in the "families of Syrian or Iraqi Christians" because they were "the most persecuted".
Television footage of migrants arriving showed that 99 per cent of them were men, she argued. "Me, I think that men who quit their country and leave their family there aren't fleeing persecution. It's obviously for economic reasons."
Front National vice-president Steeve Briois, who is mayor of the northern French town of Hénin-Beaumont, declared that none of the councils controlled by the party would accept any "illegal immigrants".
The interior ministry pointed out that the national body responsible for immigration, the OFII, decides where asylum-seekers are sent and mayors have no say in the matter.
The Paris conference, attended by representatives of about 60 countries, was to draw up an "action charter" to help members of minorities who have fled to return to the Middle East voluntarily, French Foreign Affairs Minister Laurent Fabius said before it opened.
Fabius was to jointly chair the meeting with his Jordanian counterpart, Nasser Judeh.
The decision to hold it was made at a UN Security Council meeting in March, where Fabius raised the plight of Christians, Yezidis in Kurdish regions of Iraq and Kurds in the Syrian town of Kobane.