The Congressional Budget Office said yesterday that state, local and federal governments will have to spend an additional $11 billion annually between now and 1990 to repair the nation's transportation and water- and sewage-treatment systems.

According to the CBO, governments now spend $36 billion annually, while $53 billion is needed. The federal gasoline tax increase of 5 cents a gallon, which took effect April 1, will reduce the difference about $6 billion annually, the CBO said.

The report marks the first time the CBO has tried to total the cost of repairing or building highways, public transit, water- and sewage-treatment systems, dams and other waterway investments and the airport and air traffic control networks. Some experts have placed the cost of meeting these infrastructure needs as high as $3 trillion.

The CBO also noted that government spending traditionally has favored construction over repair and maintenance, but said that now that the United States has a mature infrastructure the emphasis should shift.

In the highway program, for example, the CBO said that, since the federal government covers as much as 90 percent of the cost of construction, "current policies promote states and localities to neglect repair." Much the same argument was made by environmental groups in December, when the gasoline tax increase was debated on Capitol Hill.

The CBO also said that present federal policies, which stress the "user fee" concept, result in some users paying an inequitable share. It pointed to the small airplane and business aviation community, which places tremendous demand on both the air traffic control and airport systems and benefits greatly from the federal tax on airline tickets.

Further, the CBO said, many projects that are primarily local frequently become eligible for federal funds, "thus diverting funds from investments of national importance . . . ."

Nonetheless, the federal government has an important role to play, the CBO said, because it is "in the best position to ensure that infrastructure investment simultaneously advances national goals of efficiency and fairness."

The CBO estimates that for the next seven years the annual highway needs of all levels of government will total $27.1 billion, with federal aid under current formulas of $13.1 billion; transit $5.5 billion, with federal aid of $4.1 billion; waste-water treatment $6.6 billion, with federal aid of $4.2 billion; water resources $4.1 billion, with federal aid of $3.7 billion; air traffic control $800 million, with full federal funding; airports $1.5 billion, with federal aid of $900 million, and municipal water supply $7.7 billion, with federal aid of $1.4 billion.