The fire broke out before dawn in a building that was undergoing work, spokesman Gabriel Plus told AFP.
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.
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