Federal agencies in Virginia have received a $2 million rebate from Virginia Electric & Power Co. as a settlement of a rate increase application that was partially rejected last August by the Federal Energy Regulatory Commission, according to the General Services Administration.

In addition, eight municipalities--including the city of Manassas--and 13 cooperatives in the state have received smaller rebates under the agreement, a Vepco official said.

Vepco had filed for a rate increase affecting municipal and cooperative customers in March 1982. That rate schedule is "paired" with a separate "military schedule" negotiated with the Navy on behalf of all wholesale federal agency users in Virginia.

In December 1982, the federal energy agency awarded only part of the increase, a decision that affected the "military schedule" customers.

Vepco official John K. Taylor said the refunds appeared as credits on bills mailed last week for federal agencies purchasing their power wholesale and in February for the municipalities and co-ops.

Most of the rebate--an estimated $1,649,000--is going to military agencies using power under the auspices of the Navy. GSA will split the remaining $351,000 among its wholesale users that include the Army, Air Force, Veterans Administration, Coast Guard, Federal Aviation Administration, Postal Service, Transportation Department and GSA.

Charles Rieder, the Navy's chief negotiator, said the kilowatt-hour rate "will go down only slightly under the new agreement from the 4.5 cents per kilowatt hour . . . but because we're such a big user, that's significant." Besides the kilowatt-hour rate, energy consumption and load factors are involved in figuring the rebate.