WASHINGTON (CNN) -- A former Reagan administration national security adviser is suspected of having illegally represented the government of Sudan, which has been under strict U.S. government sanctions and a trade embargo for nearly 20 years for supporting terrorism and violating human rights.

FBI agents searched the Watergate apartment in Washington where Robert McFarlane resides seeking evidence of his alleged connection with Sudan. Court documents show agents seized handwritten notes, computer equipment and White House documents classified up to the level of Top Secret.

McFarlane, who served as President Ronald Reagan's national security adviser from 1983 to 1985, has not been charged with any crime, and the U.S. attorney in Alexandria says McFarlane is working with authorities on the case.

"Mr. McFarlane is cooperating with this ongoing investigation and through his counsel has asserted his innocence," said the prosecutor's spokesman Peter Carr.

McFarlane's lawyer did not return a call asking for comment.

The story was first reported in The Washington Post.

The detailed FBI affidavit in support of the search reviewed the history of McFarlane's alleged relationship with Sudanese officials. The investigation is more than two years old, and discloses that agents went through trash at a location in Virginia looking for clues to McFarlane's relationship with Sudanese officials.

The FBI said they had found a series of e-mails to McFarlane which agents believed to be from someone in the Sudanese intelligence service. After reviewing 2009 e-mails FBI agent Grayden Ridd said in his court document, "I believe these e-mails are evidence that McFarlane was entering into an agreement with the Government of Sudan to lobby the U.S. government officials on behalf of Sudan and to provide it with advice during negotiations with the United States."

The agent further said it appeared McFarlane and his Sudanese contact intended to structure the deal so it would appear McFarlane was representing Qatar, a U.S. ally.

McFarlane's Sudanese contact, according to the FBI, was a diplomat named Mohammed Hassen Babiker, whom the FBI said it learned was an intelligence operative for Sudan.

Babiker, the FBI says, told McFarlane the three things he was interested in discussing with the U.S. government were peace in Darfur, existing U.S. sanctions against Sudan and its inclusion on the terror list, and the role of the United States in fostering peace and unity in Sudan.

Prosecutors had no information on any legal proceedings in the case, but acknowledged they would take place in the Eastern District of Virginia.