The Census Bureau reported yesterday it has counted 99 percent of the 106 million U.S. homes on its address list, boosting the 1990 Census back on track after it got off to a slow start this spring.

Congressional aides warned, however, that although the bureau has made significant progress, it is still behind schedule in completing its door-to-door work, especially in several big cities, including Washington.

Census officials were troubled when only 63 percent of the households that received questionnaires had returned them by mid-April. They had expected the mail-back rate to be about 70 percent.

Congress appropriated $110 million in a supplemental budget to fund the additional door-to-door work necessitated by the poor mail response. Although that phase of the counting was hampered by shortages of workers in some areas, bureau officials said most of the needed workers were found after pay was increased in June.

"This milestone is a huge improvement over the mail response rate of 63 percent," Commerce Secretary Robert A. Mosbacher said in a written statement. Commerce oversees the Census Bureau.

But there are several cities where counting is still far from complete. In New York, for example, 17 percent of the door-to-door counting remains incomplete. The figure is about 15 percent in San Jose and about 11 percent in the District.

"We are very concerned about the areas where the progress is still slow," said an aide to Rep. Thomas C. Sawyer (D-Ohio), chairman of the subcommittee on census and population. But, the aide said, "after the first week in June, they've had a real turnaround in making a lot of progress."

The bureau originally was scheduled to complete its door-to-door work June 6, but that deadline was extended after it became clear the mail-back rate was so low.

Now the bureau hopes to complete its work by mid-July, the congressional aide said.

Census Bureau spokeswoman Rhea Farberman said 55 percent of the agency's district offices have completed the door-to-door counting. But she said the bureau is ahead of schedule in processing completed questionnaires.

Still unanswered is how much of the population may have been missed.

"What they're saying now is they've counted {99} percent of those who returned questionnaires and those on a list" of housing units, said William M. Hunt, assistant director of the general government division at the General Accounting Office. "That's their known universe. How many other households may still not be in that universe is still not known at the moment."

Also, census counters often are unaware of families doubled up in big-city apartment buildings or illegal immigrants who hide for fear of exposure.

The extent of the undercount will not be determined for several months, when a "post-enumeration survey" is completed and local governments will have reviewed the census numbers for accuracy. The 1980 Census undercounted the population by 1.4 percent, according to bureau estimates.