The D.C. government formally agreed yesterday to pay $50,000 in penalties for frequent violations of federal air-quality standards at the city's solid-waste incinerator on Benning Road NE and to renovate the facility to comply with the Clean Air Act.

The District also promised to spend an additional $100,000 for environmental research under a consent decree negotiated by officials of the District and the Environmental Protection Agency, (EPA) and filed in U.S. District Court.

This is the latest in a series of pollution-related agreements and fines imposed on the city by federal authorities.

Last August the District government agreed to hire 269 new employes over a three-year period and correct equipment deficiencies at the Blue Plains sewage treatment plant as a result of federal efforts to get the city to stop violating pollution standards on the Potomac River.

"Both of these settlements exemplify our commitment to a strong enforcement effort while maintaining a cooperative stance with local governments to protect the public health," said Assistant Attorney General F. Henry Habicht II, head of the Land and Natural Resources Division of the Justice Department.

Thomas P. Eichler, the EPA's regional administrator, said he was pleased with the District's commitment to solving its pollution problems.

"While incinerators provide a viable method of reducing household wastes going to landfills, we also must ensure that the burning process does not transfer a land problem to an air problem," he said.

District officials had no comment yesterday on the consent decree. Last month, Mayor Marion Barry said the city had begun a $2.25 million program to correct the problems at the incinerators months before the EPA stepped in and began negotiating the agreement.

"We do not intend to relax our efforts until tests demonstrate that we have achieved the goal of air quality toward which we are now working," Barry said at the time.

The six incinerators at the 3200 Benning Rd. NE facility operated in violation of federal particulate-matter standards since at least 1979 and were in violation of visible-emission standards during the last two years.

An EPA official said yesterday that the agency considered these "significant violations, based on size and type." Under the agreement, two of the incinerators have been permanently shut down and the remaining four will undergo substantial renovation and improvements to reduce air pollution. The work is scheduled to be completed and tested by July 1985.

The consent decree also requires interim measures for more efficient operation, improvement of long-range operation and maintenance practices, and installation of a monitoring system for visible emissions.