The fire broke out before dawn in a building that was undergoing work, spokesperson Gabriel Plus told AFP.
Read: Gunmen hold up Primark store with 10 people inside near Paris
Around 30 fire trucks and 120 firefighters were sent to the scene. Two fighters were slightly injured.
The Cite des Sciences is more a science learning centre for the general public than a traditional museum.
Located in northeastern Paris in the Parc de Villette, a redevelopment on the site of the city's former slaughterhouses, the complex draws around five million people a year.
Read: Fire in Karachi timber market extinguished after 10 hours
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ