"We are in a war against terrorism. We are not in a war against religion, against a civilisation," Valls said Friday.
New security measures will have to be taken, Valls added as the two suspected killers held one person hostage in a small town north-east of Paris.
"No escalation, no stigmatisation," said President François Hollande following a meeting of the emergency committee he has set up to handle the crisis.
The EU has also responded to the attacks.
Council of Europe president Donald Tusk called for tougher security measures, including the sharing of information on airline passengers between member states.
"Next week in Strasbourg I will appeal to the European parliament to speed up work on the EU Passenger Name Record system, which can help track the movements of dangerous individuals," said Tusk on Friday.
He also pledged to raise the question at the next EU summit on 12 February.
On Thursday former president Nicolas Sarkozy said the attack on the satirical weekly was a "war against civilisation".
Controversial author Michel Houellebecq has suspended the promotion of his new book Soumission (Submission) because of the attack.
"Time to terrorise the terrorists," was maverick right-winger Nicolas Dupont-Aignan's reaction, whhile Front National leader Marine Le Pen denounced Sunday's planned national unity march as a political manouevre because her far-right party has not been officially invited to take part.
"All citizens are welcome to the march," Hollande said on Friday after meeting with Le Pen and Dupont-Aignan on Friday morning.