A Northern Virginia man is filing a discrimination lawsuit against a federal intelligence agency, claiming it revoked his security clearance because his wife attended an Islamic school and works for a Muslim nonprofit group.

Mahmoud M. Hegab, hired in 2010 as a budget analyst for the National Geospatial-Intelligence Agency, sued in U.S. District Court in Alexandria last month. In court papers, Hegab, who lives in Alexandria, said he joined the agency in January 2010 and informed officials during his orientation that he had married Bushra Nusairat between the time of his security clearance investigation and the date he reported to work.

The NGA supplies satellite imagery to the military and requires its 16,000 workers to obtain a top-secret security clearance as a condition of employment. The agency revoked Hegab’s clearance last November, citing concerns about Nusairat’s background. Hegab, 30, was placed on unpaid leave in January.

Nusairat, 24, is a program associate with Islamic Relief USA, a global nonprofit that provides food aid and public health and educational programs in poor or disaster-prone regions and whose director advises the U.S. Agency for International Development and the State Department.

Hegab’s lawyer, Sheldon Cohen, argued in court papers that the decision to revoke his clearance “was based solely” on Nusairat’s “religion, Islam, her constitutionally protected speech, and her association with, and employment by, an Islamic faith-based organization.”

Mahmoud M. Hegab, 30, of Alexandria is a budget analyst with the National Geospatial-Intelligence Agency. His wife works for Islamic Relief USA. (courtesy Mahmoud M. Hegab)

The couple declined to comment. But Cohen, an Arlington lawyer who has represented hundreds of federal employees in security-clearance disputes, said NGA officials closely probed Nusairat’s background once they learned of Hegab’s marriage.

Cohen described Islamic Relief USA as a “noncontroversial organization,” and said he did not know of other cases in which someone lost a security clearance because of a spouse or a close relative who worked for such a group.

Several lawyers who work in security clearance agreed, saying it was the first instance they knew of in which clearance was revoked because of a spouse’s ties to Islamic organizations. Federal agencies, however, have a well-documented history of revoking clearances because of an employee’s family or marital ties.

During the Cold War, intelligence agencies regularly denied clearances to individuals whose spouses were involved with communist or “fellow traveler” organizations. People with relatives in or from Russia or other Warsaw Pact countries also were denied clearances.

More recently, agencies have rejected applicants and employees because they have family living in the Middle East or Afghanistan, said Mark F. Riley, an Annapolis lawyer who also handles security-clearance cases. Riley recalled a client who dropped legal challenges against his federal employer because he needed to travel to a Middle Eastern country to bail out an imprisoned brother.

A Fairfax native, Nusairat graduated in 2005 from the Islamic Saudi Academy, a Saudi-backed school that came under close scrutiny for using textbooks that promoted violence and religious intolerance. The school’s 1999 valedictorian also was convicted of plotting with al-Qaeda to kill George W. Bush.

Nusairat then attended George Mason University, where she studied international diplomacy and Islamic studies and led the campus group Students for Justice in Palestine.

Court papers also said that during the course of its investigation, NGA discovered a photograph believed to be of Nusairat attending a 2003 protest in Washington against the Iraq war— when she was 16 years old.

As Hegab appealed the NGA’s decision in a series of written responses, court documents said he told the agency that his wife had been born and raised in Virginia, attended the Islamic Saudi Academy because her parents believed the school provided an education on par with other ethnic and religious-affiliated schools in the Washington area, and attended the antiwar rally along with thousands of other Americans, including military veterans and lawmakers.

In March, the NGA told Hegab that he had mitigated the agency’s concerns regarding his wife’s educational background, but the agency maintained its concerns about Nusairat’s “current affiliation with one or more organizations which consist of groups who are organized largely around their non-United States origin.”

When Cohen asked the agency for further details, officials did not deny they were expressing concerns about Islamic Relief USA, he said.

Founded in 1993, Islamic Relief USA maintains offices in four states and has earned top accreditations and awards from charity auditors. Most recently, it worked with the Agriculture Department on a summer feeding program for underprivileged children and provided aid to victims of spring tornadoes in Alabama.

A charity spokeswoman confirmed Nusairat’s employment but could not comment further on the case.

“We have not received any complaints from any of our organization’s employees about discrimination when it comes to obtaining security clearances,” the group said in a statement. “In fact, because of the nature of our work, we do work closely with many federal and local agencies on a regular basis and anti-Muslim discrimination has not been a concern.”

An NGA spokesman referred questions to the U.S. Attorney’s Office in Alexandria, which also declined to comment. The Justice Department must respond to the suit by Dec. 6.

Cohen expects the government to seek a dismissal of the case. If that happens, “we’ll go on from there,” he said, “but we intend to fight.”