Embassy officials said the employee, Ahmed Alaiba, has been held with charges filed against him since Jan. 25, the New York Times reported Wednesday.
An embassy spokesman said diplomatic officials were in contact with the Egyptian government about Alaiba's status.
Since Alaiba's arrest, Western diplomats have expressed fear of retribution from the military-backed government if they keep meeting with Brotherhood officials, the Times said. Diplomats met regularly with Brotherhood leaders for decades, first when they were a minority bloc in the Parliament under ousted President Hosni Mubarak and later when they won elections in 2011 and 2012 to become the governing party.
After Morsi's ouster July 3, the military-backed government reclassified the Brotherhood as a terrorist group, and jailed Morsi, his advisers and most of the organization's leaders. Diplomats, journalists and representatives of non-governmental organizations said they don't know whether meeting with Brotherhood representatives would be considered a crime under the new government, the Times said.
The government recently filed criminal charges against 20 journalists, accusing them of conspiring with Muslim Brotherhood agents to distribute false reports about the volatile situation in Egypt. At least four of the 20 have been detained. All four worked for the Qatari-owned news network al-Jazeera.