The Environmental Protection Agency and the Department of Transportation ended months of bickering yesterday by jointly issuing guidelines on how the nation's cities should plan to clean up their air.

The events means that the cities will finally get advice from on high that they have been expecting since Febuary. Under the Clean Air Act amendments of 1977, the big cities must submit to the federal government by Jan. 1 their plans for controlling auto-related smog.

The joint guidelines, accompanied by a memorandum of understanding that defies the turf for both agencies, was praised as a "common sense approach to transportation and air quality planning" by Jack Watson, special assistant to the president.

Local officials, who have not seen the final guidelines but have received several early drafts, saud yeaterday that anything is helpful that reduces the amount of coordination they have to achieve with various federal agencies.

Both DOT and EPA have key roles to play in smog control: DOT because it has planning money in the first instance and because it can provide federal funds for solutions such as more mass transit in the second. EPA must decide whether cities are doing what they should to meet air quality standards, then has the power to sue if they do not.

Under the Clean Air Act amendments, cities must meet federal air quality standards by 1982. If they cannot, they can apply for a five-year extension. During that extension they must begin mandatory inspection and maintenance programs for automobile pollution control equipment, among othe things.

Barbara Blum, EPA's deputy administrator, said that "we currently expect a number of our largest cities to request extensions until 1987." She listed Washington, Los Angeles, Philadelphia, San Diego, Baltimore, Milwaukee, Denver, San Francisco, New York, Chicago, Detroit and Pittsburgh as the most likely candidates.

Watson and David hawkins, the EPA's assistant administrator for air quality and waste management, both said that nothing in the joint agreement should or could be construed to mean that transportation plans are one of those environmental areas where regulation will be relaxed because of alleged inflationary impact.

Earlier this week the EPA slightly increased the level of smog that will be permitted in air over the nation's cities. That slight change, Hawkind said, could save as much as $1 billion in auto emission and other cleanup costs.

Robert S. Strauss, the president's special counsel on inflation, drew the wrath of environmentalists in April when he said that environmental regulations, the Teamsters and the postal workers all deserved special anti-inflation attention.

The joint transportation guidelines will be anti-inflationary, Watson said, in the sense that they reduce "the cost of doing business - the cost of filling out forms."

That is because they are written in such a way as to encourage regional EPA and DOT officials to give final approval to transportation plans instead of requiring Washington-level assistance

Nonetheless, if there is a dispute between regional EPA and DOt officials on on a city's plan, the final decision rests with Transportation Secretary Brock Adams. The EPA is always free to sue.

DOT Assistant Secretary Chester Davenport said that "a strong cooperation effort is most important where programs are independent." In addition to better public transit, he cited car pool programs and special lanes for buses and car pools as transportation answers to air quality problems.

Watson and the Office of Management and Budget, according to officials from both EPA and DOT, were particularly firm in insisting that the two agencies - old antagonists on a number of issues - come to agreement on the urban transportation question.