Pollution is a sensitive topic in China, with thousands of protests sparked every year by concerns about environmental degradation, particularly from factories.
Four districts in the capital, which has been hit by bouts of choking smog this winter, will be required to shut down 2,500 companies by the end of the year, with more scheduled to be closed next year, Reuters reported.
Quoting an unnamed official, it said rising numbers of small polluting sources such as restaurants, hotels and garages offset the impact of a dramatic fall in the number of heavy polluting and high energy-consuming companies in the city.
Last month Beijing issued its second ever "red alert" over heavy air pollution, closing schools and banning outdoor construction.
On Saturday the environment ministry cautioned that heavy smog would return next week to Beijing, the province of Hebei and nearby Tianjin.
Official data showed Beijing's average PM2.5 reading in 2015 was 80.6 micrograms per cubic meter, 1.3 times more than the national standard, Xinhua said.
China has vowed to slash coal consumption and shut down polluting industries, but environmental officials admit the country is unlikely to meet state air quality standards until at least 2030.