More than half the 5,016 primary ballots disqualified by the D.C. Board of Elections and Ethics were cast by properly registered voters, elections officials said yesterday.

Elections workers counted 2,859 requalified ballots yesterday afternoon, clearing the way for the board to certify the election results today, one month after the Sept. 14 primary, marking one of the longest vote-counting periods for a mayoral primary election since home rule began. The additional ballots are not expected to affect the outcome of any primary races.

David Splitt, the board's acting executive director, said the number of erroneously disqualified ballots was unacceptably high, but added: "That's why we rechecked. We knew the original number disqualified was too high."

A total of 125,400 ballots were cast in the primary election. Of those, 22,204 were special challenged ballots cast by voters whose names were missing from the computer rolls at their voting precincts. Two weeks ago, after reviewing those special ballots, the board said 5,016 of them would not be counted because the registration of the voters who cast them could not be verified.

After receiving hundreds of complaints from properly registered voters whose ballots were disqualified, the board directed its staff members to double-check their work. At the time, board chairman Albert J. Beveridge III predicted that several hundred ballots would be found to have been wrongly disqualified. The second check, completed yesterday, showed 2,859 had been improperly rejected.

Yesterday Beveridge said he was not alarmed at the high number of mistakes made in the first check. "This just shows the board may be slow, but it has counted the vote of every qualified voter," he said.

A total of 2,157 ballots, less than 2 percent of the total cast, remain disqualified and will not be counted, Splitt said.

Most of the finally rejected ballots were cast by voters for whom the elections board could find no evidence of registration in either its voter card file or its master computer list. In other cases, the special ballots were not counted because they were not signed, were illegible or lacked certain information such as the voter's party affiliation.

Splitt said that elections workers had used too narrow a standard for qualifying the 20,204 challenged ballots the first time they checked them against the board's files.

In that first check, ballots were disqualifed if elections workers could find no voter registration card for the people who cast them. The card file is technically the only legal record of registered voters in the city.

But in the second check, the board also counted the ballots of those voters whose names appeared on the computerized list of registered voters used in the 1981 school board election -- even if those names were not in the card file.

Elections officials said they decided to use the 1981 list because they knew it contained the names of several thousand properly registered voters whose names were dropped from voter rolls when the board switched to a new computer system in July.

The second check also turned up a number of voter registration cards that were indeed on file but had apparently been missed in the first check.

One of the reasons elections officials switched to the new computer system was because the old system contained so many inaccurate or incomplete voter listings. Splitt revealed yesterday that he has since found several cases in the new computer system where voters were listed in the wrong precincts. He said he expects to correct the errors by the November general election.

Splitt said the board is currently working to ensure that the voters whose names were dropped from the rolls in the primary will appear on the lists in the Nov. 2 general election.

He said the board is also considering publishing in the newspaper the names of the voters whose ballots were originally disqualified and subsequently counted. He said computerized lists of voters will be placed in local libraries in the coming weeks so that voters can check to see whether they are on the rolls, and can clear up any problems, before the election.