"The fire hit about 200 square metres (2,150 square feet) of the roof and the attic," Prague fire brigade spokesperson Pavlina Adamcova told AFP, adding the museum's collections were not affected.
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One security guard suffering from smoke inhalation was taken to hospital.
"The fire was reported at 0032 GMT. We had it under control about two hours later," said Adamcova, adding the cause of the fire and the extent of the damage were under investigation.
The sprawling neo-Renaissance building, a dominant feature of many a picture postcard from Prague, was built in 1885-1891.
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It is currently undergoing an extensive reconstruction worth over 1.35 billion koruna (50 million euros, $56.5 million), which started in 2011 and is due to be completed in 2018.
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