Czech media said the shooting had occurred at Charles University's Faculty of Arts, whose teachers and students were instructed to take shelter as police action was under way.
"The gunman was eliminated!!!" police said on X, formerly Twitter.
"The building is currently being evacuated and there are several dead and dozens of wounded people on the scene," the statement added.
Interior Minister Vit Rakusan told public Czech TV the gunman was "probably dead", citing "preliminary information".
Prague's emergency service said on X that "a large number of ambulance units" were deployed at the faculty, adding the injuries ranged from light to very serious.
The private Nova TV reported a blast and a gunman on the roof of the building in Prague's historic centre.
Rakusan said "no other gunman has been confirmed" and called on people to follow police instructions.
Police closed the area and asked people living nearby to stay at home.