Germany's Konrad-Adenauer-Stiftung, a think tank close to Chancellor Angela Merkel's conservatives which promotes democracy abroad, said on Thursday authorities in Abu Dhabi had ordered it to shut its office there.
"We can only react with complete incomprehension at this unexpected and sudden development in Abu Dhabi," said foundation head Hans-Gert Poettering in a statement.
No reason for the closure had been given, he said. The Foundation opened its office in the capital of the United Arab Emirates in 2009.
"After our experience in Egypt, not only do we regret this decision but it rings alarm bells if non-governmental organisations and political foundations are not desired in the Arab World," added Poettering.
Egyptian prosecutors and police raided the foundation's offices in Cairo last year, along with those of several other foreign pro-democracy and human rights groups.
German Foreign Minister Guido Westerwelle regretted the decision, said his spokesman.
The reasons for the closure order were not immediately known and UAE officials were not available to comment.
"Foreign Minister Westerwelle has personally pushed for a rethink of this decision with the UAE's foreign minister ... in the last few weeks and again on the sidelines of the nuclear summit in Seoul," said Westerwelle's spokesman.
Germany has boosted its economic ties with Abu Dhabi in the last few years with sovereign wealth fund Aabar Investments buying stakes in German companies, most notably in carmaker Daimler.