Cruise, 41, co-producer and star of "Mission: Impossible 3" was in the German capital last month to scout out locations for the sequel, due to start filming later this year.
One of his favourite locations was the 40-metre (130-feet) diameter dome on the top of the parliament building, said a spokesman for the Studio Babelsberg production firm near Berlin, which is working with Cruise to find locations.
But the German parliament turned down the request to film there.
"The building is not available as a film location and we refuse point blank every request to use it as such," said a spokesman for Parliament President Wolfgang Thierse.
"It is about maintaining the dignity of the parliament."
The 19th-century Reichstag has been a major tourist attraction since British architect Norman Foster gutted the building, which was damaged in World War Two, and turned it into a model of transparency with the glass dome.
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