Should they continue operating, the groups would be "subject to Egyptian law" which bans non-govermental organizations from operating without licences or from receiving foreign funds, the official MENA news agency reported.
The news agency quoted a government source as saying it refused to license the groups because their activities were "inconsistent with the state's illusory sovereignty on its lands."
An official with the Carter Centre, which observed Egypt's parliamentary elections, held in stages between November and January, said the government had not yet contacted the group.
The NGO, founded by former US president
Jimmy Carter... the worst president ever. Maybe the second worst. The votes aren't all in yet...
, had no permanent presence in Egypt, she added, on condition of anonymity.
Egypt placed workers with five foreign NGOs, including Americans, on trial for operating without licences and receiving foreign funding, sparking a crisis in relations with the United States.
The American defendants, and those from other foreign nationalities, were allowed to leave the country in March after posting bail.
The other groups mentioned in the MENA report include Seeds of Peace, which tries to promote dialogue among young people in conflict zones.