The State Department has always been tight-lipped about who receives democracy funding for Iran, out of fear that the groups’ associates would be targeted in Iran. It is unclear how many other groups have lost their funding under the Obama administration.

“US government priorities for the region continue to include support for civil society and advocacy, promoting the rule of law and human rights, and increasing access to alternative sources of information,’’ Edwards said. “Applications submitted to USAID are thoroughly reviewed against the evaluations criteria outlined in its solicitations.’’

The job of doling out money to groups seeking to influence Iran has been shifted from the State Department’s Near Eastern Affairs Bureau to a lower-profile division, its US Agency for International Development. USAID spokesman Harry Edwards did not provide an explanation of why funding was denied for the Human Rights Documentation Center, widely seen as the most comprehensive clearing house of documents related to human rights abuses in Iran. He said the government’s funding priorities have not changed.

Michael Rubin, a scholar at the American Enterprise Institute, a conservative Washington-based think tank, said, “It is a shock that they did not get funding.’’ A reason, he asserted, may be that “the Obama administration is so focused on engaging Iran that they don’t want this information to get in the way.’’

“The Iran Human Rights Documentation Center is at the forefront of pioneering and vitally important work,’’ said Senator Joe Lieberman, a Connecticut independent, in a statement yesterday. “It is disturbing that the State Department would cut off funding at precisely the moment when these brave investigations are needed most.’’

Many see the sudden, unexplained cutoff of funding as a shift by the Obama administration away from high-profile democracy promotion in Iran, which had become a signature issue for President Bush. But the timing has alarmed some on Capitol Hill.

“If there is one time that I expected to get funding, this was it,’’ said Rene Redman, the group’s executive director, who had asked for $2.7 million in funding for the next two years. “I was sur prised, because the world was watching human rights violations right there on television.’’

But just as the Iran Human Rights Documentation Center was ramping up to investigate abuses of protesters after this summer’s disputed presidential election, the group received word that - for the first time since it was formed - its federal funding request had been denied.

WASHINGTON - For the past five years, researchers in a modest office overlooking the New Haven green have carefully documented cases of assassination and torture of democracy activists in Iran. With more than $3 million in grants from the US State Department, they have pored over thousands of documents and Persian-language press reports and interviewed scores of witnesses and survivors to build dossiers on those they say are Iran’s most infamous human-rights abusers.

Obama officials have argued publicly for a less-confrontational approach than Bush, in the belief that the Bush administration’s vocal support for democracy activists made them targets in Iran and stirred up fears of regime change.

The Obama administration has emphasized other forms of assistance, such as aid for software programs that help activists communicate on the Internet anonymously. It also has continued funding for exchange programs. In the coming months, for instance, the administration hopes to bring Iranian lawyers to major cities in the United States, including Boston, to talk with American lawyers about their concept of law.

Formed by two exiled Iranians in 2004 with a $1 million grant from the State Department, the center made its home near Yale’s campus, where it attracted Yale law school professors to its board. The board also includes the dean of Harvard Law School, Martha Minow.

The group has published 12 reports in English and Persian about the forced confessions of detained bloggers and journalists, the 1988 massacre of thousands of political prisoners, and the Iranian government’s campaign to assassinate dissidents abroad. Although the State Department has been the group’s main source of funds, the Canadian government granted it money to research human-rights abuses in the wake of the disputed election this year.

Currently, the group is working to develop a list of all those who were arrested following the election and a list of those responsible for alleged abuses in prison. But without additional funding, the group will shut down in May when its funding runs out, Redman said.

The group is not affiliated with any political party in Iran. It attracted controversy during its early years, however, when one of its founders and current board members, Ramin Ahmadi, gave a workshop in Dubai on tactics of underground political resistance to Iranian citizens who had secretly traveled there.

Since then, the Iranian government has accused Ahmadi of being an agent of the United States, and some of his trainees were arrested. Ahmadi, a medical doctor in Danbury, Conn., still vocally supports the opposition movement, joking at a recent panel at Yale Law School that he could sneak audience members into Iran if they wanted to join.

But at least three other groups that received funding under Bush’s democracy program for Iran have been told they would not receive funding this year, according to Roya Boroumand, founder of the Bormound Foundation, which works against the death penalty in Iran. Boroumand said her group does not get State Department funds, but that she is in contact with other organizations who do, and all are worried.

“If the rationale is that we are going to stop funding human rights-related work in Iran because we don’t want to provoke the government, it is absolutely the wrong message to send,’’ she said. “That means that we don’t really believe in human rights, that the American government just looks into it when it is convenient.’’

© Copyright 2009 Globe Newspaper Company.