"How could president (Vladimir) Putin be thrilled that we have the military base at Deveselu with ballistic missiles", Mihai Fifor said Tuesday during a live interview with a local television station.
Fifor later blamed "a misunderstanding or an error of communication".
"No one could ever say that there are ballistic missiles at Deveselu. I said that the base is a defence against ballistic missiles, not that it has any of them," Fifor told another news channel.
Russia sees the missile shield as a security threat on its doorstep, despite the US and NATO insisting it is not aimed at undermining Moscow's defences.
According to NATO, the shield is a purely defensive system equipped with interceptors, which can protect NATO members against short- and medium-range ballistic missiles.
Romania's main opposition parties, the National Liberal Party and the Save Romania Union, have called on Fifor to quit. Former president Traian Basescu of the People's Movement Party also condemned Fifor.
"Mihai Fifor has no place in the government... He confirmed statements made by Putin and other officials who try to undermine the reality, which is that Deveselu is a defensive missile system, not on offensive one," Basescu wrote on Facebook.
Fifor's comments follow two other gaffes.
Prime Minister Viorica Dancila declared last week she was "happy to be in Pristina" while visiting Montenegro's capital Podgorica. Pristina is the capital of Kosovo, which Romania does not recognise.
And Romania's agriculture minister apologised last week for having compared the incineration of dead pigs infected with African swine fever to the Auschwitz concentration camp.
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