The Egyptian ambassador to Germany was told to report to the Foreign Ministry on Friday.
Foreign Minister Guido Westerwelle said he expected an explanation for the raids, which people on the ground said were designed to intimidate those working for human rights in Egypt.
He is expected to tell the Egyptian ambassador that the incident must be cleared up as fast as possible, and that the Konrad-Adenauer Foundation be allowed to continue its work without further harassment, the Süddeutsche Zeitung reported.
Egyptian media said on Thursday that state prosecutors had carried out the raids accompanied by police to look for evidence that the organizations concerned had been working without licenses, or that they had been bringing money into the country from abroad.
But Egyptian human rights groups said the raids were part of a campaign of intimidation and that police had seized documents and computers. They said such raids would not even have been carried out under the rule of former dictator Hosni Mubarak who was deposed in February, the Süddeutsche Zeitung said.
Konrad-Adenauer Foundation chairman Hans-Gert Pöttering said things had to be put right in Cairo. “These events irritate us greatly and I call on the responsible Egyptian authorities to re-establish the capabilities of our Cairo office immediately.” He said the unhindered work of non-governmental organisations were crucial for democratic and law-abiding developments in Egypt.
Mubarak's trial resumed this week after a three-month break. He is charged with ordering the killing of about 850 people during the protests which eventually toppled him.
Other foreign institutions including the two American groups, the National Democratic Institute and the International Republican Institute, were also raided according to Human Rights Watch. The American government has said it was deeply concerned by the reports and the Egyptian ambassador to the US is also expected to be called in for a dressing down.