All the primates have been returned to their pens with the exception of "an elderly female, a young female and a baby", said Sophie Ferreira-Le Morvan, the deputy head of the National Museum of Natural History.
They remain in the area of the "grand rocher", a landmark central mountain inaccessible to the public at the Paris zoological park in the Vincennes area of the French capital.
The three baboons are "under surveillance", Ferreira-Le Morvan said, and the zoo will not reopen until they are captured.
Safety procedures were "immediately" triggered, the zoo said in a statement, with a total of 60 firefighters, 20 police and all of the zoo's staff mobilised to capture the animals.
None of the baboons reached public areas and the evacuation was ordered as a precaution, the zoo said. Click for more trending news
Follow NDTV for latest election news and live coverage of assembly elections 2019 in Maharashtra and Haryana.
Subscribe to our YouTube channel, like us on Facebook or follow us on Twitter and Instagram for latest news and live news updates.