"Our deepest condolences and sympathies go out to the victims and their families," said the Indonesian Ministry of Foreign Affairs in a statement issued on Thursday.
"The Indonesian Embassy in Paris and Consulate General in Marseilles are actively in coordination with relevant authorities on the ground," it stated.
According to the Indonesian government, there were no reports of Indonesian casualties in the knife attack.
A lone attacker armed with a knife entered the Basilica of Notre Dame in the city centre on Thursday morning local time. A man and a woman died at the scene, while another woman died from her injuries. The attacker was injured after being shot by police and taken to hospital.
French authorities are treating it as a terrorist incident.
Tensions and instances of intolerance are growing in France following French President Emmanual Macron's remarks abour Islam and the re-publication of the satirical caricatures depicting Prophet Muhammad.