Piotr Müller's statement came after Ryszard Terlecki, a senior lawmaker with the governing Law and Justice (PiS) party, said a day earlier that Poland could be forced to "search for drastic solutions" if the EU did not take on "a shape that is acceptable to us."
According to some commentators, Terlecki was implying Poland could make an exit if the EU crossed a certain line.
Müller on Thursday said emphatically that "Poland will not be exiting the European Union" when asked to comment on Terlecki's remark in a media interview.
"We want Poland to be a member of the EU, but we also want to play an active role in the bloc," Müller told an online broadcaster.
"We have our rights, too, in the EU and in the legislative process, and we should make use of them," he added.
'We won't follow in Britain's footsteps'
Asked if he could give assurances Poland would not follow the UK out of the EU, Müller responded: "We won't follow in Britain's footsteps because it is not advantageous for us."
He added that being a member of the bloc "made Poland wealthier, brought the benefits of trade" and made the country "more secure geopolitically."
"But regardless of that, we must raise our own voice in the EU and oppose certain things," Müller said.
Terlecki told an international business conference in Poland on Wednesday that the EU "should have a shape that is acceptable to us because if it maintains its likely course, then we must search for drastic solutions."
He added that "the British showed they wouldn't abide by the dictatorship of the Brussels bureaucracy, and they turned around and left."
"We don't want to leave, as support for the EU is very strong in our country, but we can't allow ourselves to be pushed into something that will limit our freedom and constrain our development," Terlecki also said in Karpacz on Wednesday.
The Economic Forum in Karpacz, dubbed the "Polish Davos," is a three-day annual conference that was previously held in Krynica, another mountain resort in southern Poland.
This year, more than 3,500 guests from around the world have converged on Karpacz, including senior politicians, parliamentarians, business executives and culture leaders.