RIYADH, Saudi Arabia — As Secretary of State Hillary Rodham Clinton worked hard on Saturday to focus attention on deepening security ties with the Arab nations of the Persian Gulf, she found herself having to deal with a surprising act of diplomatic defiance: the decision by the United Arab Emirates, an ally, to shutter the offices of an American-financed group that promotes democracy.

So far, the U.A.E. have not publicly explained their actions against the organization, the National Democratic Institute, which only recently was one of several nonprofits prosecuted in Egypt amid concerns about what many Egyptians perceive as foreign meddling.

The move by the U.A.E. was not as shocking as that by the Egyptians — in that case, the son of a Cabinet member was charged in criminal court. But it was especially provocative, coming just before Mrs. Clinton arrived in the region for talks with the U.A.E. and other members of the Gulf Cooperation Council.

Egypt’s investigation of the group, along with the International Republican Institute and others, prompted a fierce debate in Washington over whether to continue providing military assistance to the Egyptian military. The Obama administration eventually allowed $1.3 billion in arms sales to move ahead, but only after Egypt allowed American employees of the groups to leave the country.

The State Department on Saturday defended the National Democratic Institute’s work in the U.A.E., while an official with the group in the United States expressed some bafflement since he said it did not do democracy-building work in the country. Les Campbell, the regional director for the Middle East and North Africa, said the office in Dubai, one of the emirates, was used to coordinate work in nearby countries, including Saudi Arabia.

A German organization that was also targeted in Egypt, the Konrad Adenauer Foundation, recently closed its office in the U.A.E. at the demand of the country’s foreign ministry.

The closing of democracy-building organizations cast a shadow on the meeting here Saturday, which was intended to inaugurate a strategic multilateral alliance with the nations in the Gulf Cooperation Council. In addition to the U.A.E., the group includes Saudi Arabia, Kuwait, Bahrain, Qatar and Oman.

Mrs. Clinton said the alliance would create “opportunities to pursue multilateral cooperation on shared challenges, including terrorism, nuclear proliferation and piracy.” As with Egypt, though, she found herself defending American nongovernmental organizations, or N.G.O.’s, in countries that are important to the United States on security matters.

When pressed during a news conference about the closing, Mrs. Clinton said “we very much regret it” and said she had brought it up with the country’s foreign minister at the conference.

“Both N.D.I. and the Konrad Adenauer Foundation offices play a key role in supporting N.G.O.’s and civil society across the region, and I expect our discussion on this issue to continue,” she said.

She added, however, that the administration’s “overarching” interest was to cooperate with countries in the region, particularly in the areas of security and antiterrorism.

The idea for Saturday’s meeting took shape last fall as the Obama administration moved ahead with its withdrawal of the last American troops from Iraq, reducing the American military presence in the region at a time of increasing tensions with Iran.

The United States has close bilateral military relations with all six gulf nations, but the administration hopes to develop a more united military strategy that would include an integrated missile defense system, intended to combat any attack in the region from Iran.

The United States has recently stepped up arms sales to gulf nations, including a $30 billion sale of 154 F-15 fighter jets to Saudi Arabia and a nearly $2 billion one to provide the United Arab Emirates with one of the most sophisticated antimissile systems.

The gulf council, dominated by Saudi Arabia, has become more active beyond its borders. Qatar and the U.A.E. sent combat aircraft to the Mediterranean last year as part of the intervention against Libya, while Bahrain and the U.A.E. have forces in Afghanistan.

That has made the United States eager to work even more closely with the nations as a group. At the same time, however, the gulf nations are some of the least democratic in the world. Last year, the gulf council dispatched a military force to Bahrain to support that government’s suppression of popular protests, brushing aside American criticism. (Critics of the Obama administration’s policy in Bahrain argue that the United States, which bases its Fifth Fleet there, did not itself press the country hard enough to end a brutal crackdown.)

Mr. Campbell of the National Democratic Institute said the group had been working in Dubai for almost four years. On Wednesday, he said, authorities visited the office and said the license had been canceled, but did not say why.

He said the office helped support programs in countries including Qatar and Kuwait and that many of its programs worked with women to bolster their leadership skills. He said the organization had two expatriates and two local staff members in Dubai.

“I don’t know if this is part of a pattern after Egypt, but we’re disappointed and disturbed at this turn of events,” he said.

Sam Gejdenson, a former House Democrat from Connecticut who serves on the NDI board, said that certain players in the Middle East may have felt threatened by the activities of the regional office.

“Sometimes there are factions in a country that try to convince themselves if they can hold things together, everything will pass and be okay,” he said, adding that he was not speaking on behalf of NDI. “So they lash out at organization like NDI that try to help bring about fair and honest elections. But you pay a heavy price in the long haul for such a move.”

Mrs. Clinton also confirmed Saturday that Iran and six world powers, including the United States, had agreed to meet in Istanbul on April 13 for the latest round of talks about Iran’s nuclear program.

Thom Shanker and Eric Lipton contributed reporting from Washington. (Copyright 2012 The New York Times Company 04/01/12)