The Konrad Adenauer Foundation said it was forced by the UAE government last week to stop its work in Abu Dhabi, where it opened an office in 2009. It said it had received "no understandable explanation" for the move.
It was the second time in three months that the foundation saw one of its foreign offices shuttered, following a similar step in Egypt in late December.
The think tank this week termed the decision an "alarm bell for democratic development in the Arab world".
Foreign ministry spokesman Andreas Peschke said the UAE's ambassador to Berlin had been invited for talks Friday at the ministry to underline the "positive work of the foundation" and seek a "common solution" to reopen the Abu Dhabi office.
"It is our goal to find a way together with the United Arab Emirates for this to happen," Peschke told a regular government news conference.
"But whether and how this could happen I cannot say at this time."
He declined to draw a parallel to the decision in Cairo. "The situations in the individual countries are too different," he said.
Merkel said Thursday that she "regretted" the decision and that Germany would "attempt to maintain close cooperation with the United Arab Emirates".
"However we of course wished that the Konrad Adenauer Foundation could continue its work there," she told reporters.
Foreign Minister Guido Westerwelle said he had personally asked his Emirati counterpart to revisit the decision.
More than 40 representatives of international groups promoting democracy are on trial in Egypt charged with illegal financing and other infractions, including two employees of the Konrad Adenauer Foundation.