He was speaking after Germany announced that it was re-imposing border controls with Austria, in the wake of a flood of migrants passing through that country.
Though on the campaign trail for next month's general election, he spoke as prime minister in making the comment.
"The Schengen accord foresees that, for reasons of safety and in exceptional circumstances, the accord may be temporarily lifted," Passos Coelho said. "Now it must be assessed whether, in the present circumstances, the rules foresees are being respected, and it is up to the European Commission to make that assessment."
The prime minister reaffirmed that "Europe has a problem and countries need to do more to receive refugees, but this must be done in safe conditions." He referred to the "avalanche of refugees" arriving in Germany through Austria.
"Germany has a very open position to receive refugees, but it is natural that, also for security reasons, it is necessary temporarily to take measures that make it possible to identify people and prepare their reception," he said.
According to the Portuguese prime minister, "the image that Europe must given the world is one of receiving these refugees with dignity and security for the European space - refugees who are looking in Europe for a place of safety in fleeing war."