"Welcoming refugees who are fleeing war is part of our duty," he said following a meeting with his new German counterpart, Sigmar Gabriel. "We must... ensure that this happens in a fair, just way and with solidarity."
Trump on Friday signed a sweeping executive order to suspend refugee arrivals and impose tough controls on travellers from seven Muslim countries.
"This decision can only cause us concern. But there are a lot of other issues that are causing us concern", Ayrault, with Gabriel at his side, said when asked by journalists about the restrictions.
He and Gabriel discussed "at length what we are going to do."
The pair plan to contact the nominated secretary of state, Rex Tillerson, once he is confirmed, "to discuss the issue point by point and have a clear relationship."
"Clarity, coherence and if necessary firmness are needed to defend our beliefs, our values, our vision of the world, our interests, French, German and European."
Gabriel on is on his first foreign trip since being appointed on Friday to replace Frank-Walter Steinmeier.
A spokesman for the European Commission, the EU executive said it had "no comment to make" on Trump's move.
But he recalled "comments made several times by" European Commission President Jean-Claude Juncker, "that Europe is and remains open to all those who flee armed conflicts and terror, whatever their religion."