"Terrorism is so well organised that it does not need to take the difficult route taken by the refugees, who risk their lives by crossing the high seas," Ursula von der Leyen told reporters.
"So I would advise that we be cautious about mixing the idea of terror with refugees," she said.
"These refugees have fled from precisely this type of barbaric terror, and they have fled to our region because they have been persecuted by the so-called Islamic State or by (Syrian President Bashar) al-Assad in a unbelievable way," she said.
Von der Leyen was joined in her appeal by Justice Minister Heiko Maas, who called for "very, very great prudence, until things are clear".
"We are aware that the IS (Islamic State) is known to leave such false tracks behind to politicise and radicalise the issue over refugees in Europe," Maas told public broadcaster ARD.
On Twitter, the Justice Ministry shared further comments from Maas, who said that "refugees are victims and not perpetrators.
"Our answer to terror must be to offer its victims protection."
Von der Leyen's remarks came after France's Justice Minister Christiane Taubira said on Sunday that a Syrian passport found near one of the Paris attackers' bodies, which had been used to register as a refugee in Greece, was a fake.
Important. Minister Justice France: the Syrian passport was a fake. "Daesh is playing politics". https://t.co/vCLlVU0tky— Gauri van Gulik (@GaurivanGulik) November 15, 2015
Many commentators have warned that further dividing opinion over refugees arriving in Europe was among Isis' aims in the attacks.
The group is reportedly furious that so many people fleeing violence in the Middle East have turned to Europe rather than to them for support, despite its best efforts to convince them otherwise in a series of videos published online.
You know what pissed off Islamist extremists the most about Europe? It was watching their very humane, moral response to the refugee crisis.— Iyad El-Baghdadi (@iyad_elbaghdadi) November 14, 2015
Germany's Interior Minister Thomas de Maiziere had already made a plea not to link refugees to the terror attacks that claimed 129 lives in Paris late Friday.
"I would like to make this urgent plea to avoid drawing such swift links to the situation surrounding refugees," de Maiziere said on Saturday, noting that there have already been "appalling scales of attacks against asylum seekers and asylum seeker shelters".
Besides beefing up police presence and border controls, the interior minister said after a crisis cabinet meeting that security forces will also keep a close watch on far-right extremists.
Germany is expecting up to one million asylum seekers this year, but the influx has also exposed fault lines in the country, with a spate of arson attacks on refugee shelters.
Bavaria pounces on Paris
Critics of the open-door policy for those fleeing war also stepped up their calls to halt immigration, following the Paris attacks.
Bavaria's premier Horst Seehofer, who has been among the fiercest critics of Chancellor Angela Merkel's welcoming stance to refugees, on Saturday reiterated a call for reinforced checks at Europe's external borders as well as at each European country's national border.
The southern region's finance minister Markus Söder meanwhile told the Welt am Sonntag newspaper that many asylum seekers have entered Germany through what are known as green borders – woods - and are therefore not registered by border forces.
"We can't not know who is coming to Germany and what these people are doing here. We must stop this situation with all our means," he said.
"Not every refugee is an IS terrorist. But to believe that there is not a single fighter who counts among the refugees is naive," he said referring to the Islamic State group.
"France shows that in the question of security, we must make no compromise," added Söder.