The regional secretary of the police union Alliance told BFM TV that one officer was hit in the head with the hammer, prompting police to fire at the attacker.
The man shouted "this is for Syria" as he attacked, according to French interior minister Gerard Collomb.
Two police sources cited by Reuters said the officers shot the man in the thorax after he attacked.
The attacker had also threatened passers-by before targeting the two police officers, according to BFM TV.
Collomb said the man carried the identity card of an Algerian student and appeared to have acted alone.
Paris police initially tweeted that an "intervention" was taking place in the square in front of the cathedral, and asked people to avoid the area.
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