CAIRO — The U.S. Embassy in Cairo is giving shelter to three U.S. citizens to protect them from potential arrest by the Egyptian authorities as part of a politically charged investigation into the activities of four U.S.-backed nongovernmental organizations operating here, colleagues said Monday.

The decision to give the individuals shelter is a new low in the relations between Cairo and Washington, which recently threatened to stop its $1.3 billion in annual aid to the Egyptian military if it fails to take steps toward a democratic opening, including respecting such nongovernmental groups.

Word of the decision came as Egypt’s ruling military council began taking steps to address its fraying relations with Washington by sending a delegation of officers to the United States for meetings this week with their military counterparts, legislators and other officials. The delegation was in Tampa, Fla., on Monday, visiting the Central Command headquarters.

Officials at the U.S. Embassy declined to comment on the decision to shelter the Americans, first reported Monday in The Washington Post. The reports followed the disclosure last week that the Egyptian government had barred at least a half dozen U.S. employees of the groups from leaving the country.

Those employees work for the International Republican Institute and the National Democratic Institute, two democracy-building groups with close ties to U.S. congressional leaders. The groups have come under a criminal investigation by the Egyptian authorities over allegations that they violated rules on foreign funding.

It was unclear how many of the Americans had sought refuge in the embassy. One source, speaking on the condition of anonymity, said there were three, all from the International Republican Institute, who had become concerned because of press reports that the investigation was nearly completed and that they could face arrest. It was also unclear what could happen if the Egyptian authorities pressed charges, since the sheltered Americans do not have diplomatic immunity.