Ursula von der Leyen sparked the row when she told a German television talk show that “the healthy democratic resistance of the young generation in Poland needs to be supported”.
Appearing on the show Thursday, Von der Leyen applauded Poland and the Baltic countries' fight for independence during communism and successful bids to join the European Union.
She also insisted that the countries of that region must not be left out of changes taking place in the EU.
However, Poland has recently faced EU concerns that the right-wing Law and Justice (PiS) government's controversial court reforms, which have sparked street protests, will erode judicial independence in the former communist state.
Berlin later claimed the minister's comments had been taken out of context.
Poland's defence ministry summoned the German military attache over the remarks, but did not accept his explanation.
Ministry spokeswoman Anna Peziol-Wojtowicz told reporters Monday: “The Polish defence ministry considers it unacceptable that a minister of a NATO alliance member is calling the citizens of another state to anti-government activity.”
A German defence ministry spokesman said Monday: “I am under the strong impression that the quotes that sparked excitement in Poland at the weekend were ripped out of context and were changed in social media.”
Polish Foreign Minister Witold Waszczykowski later appeared to downplay the spat on Monday, saying Warsaw “does not want to start a big political debate”.
He repeated however that “a country that is a friend and an ally within EU and NATO should not be disciplined” by German politicians, “especially considering the delicate ties” between the neighbouring countries.
Relations between Poland and the EU and Germany have been strained since German Chancellor Angela Merkel said in August that Berlin could “not stay silent” on EU fears about the rule of law in Poland, calling it a “serious issue”.
There have also been tensions over the PiS government's decision to revive the issue of war reparations which it believes Germany owes Poland – an issue that for years had been considered settled.