The congregations said they would affiliate with the Anglican Church of Uganda or the Anglican Church of Nigeria, by way of the Anglican District of Virginia, the Episcopal News Service reported.
The Anglican District of Virginia is part of the Convocation of Anglicans in North America.
Two of the congregations minister to the Washington elite and occupy real estate worth $27 million, The New York Times reported. The development could lead to a legal battle over possession of the property.
Bishop Peter Lee of the Episcopal Diocese of Virginia said that, as of Sunday, Nigerian and Ugandan congregations were "occupying Episcopal churches."
Presiding Bishop Katharine Jefferts Schori said last week she was saddened by the prospect of a split.
"These departures are taking place in most mainline denominations, and are an expression of the anxiety of our times and the discomfort many people feel in trying to live in tension," she said.
The bishop called the move a "quick fix" and said it would not be "an ultimate solution for our discomfort."