SAN FRANCISCO (Map, News) - Although Mayor Gavin Newsom is the presumed to be the winner of this election — even by his political rivals — a complete tally of votes is not expected for several weeks, due to problems with San Francisco’s voting machines.

Newsom had the advantage of being the incumbent, the strength of $1.8 million in campaign contributions and political clout unmatched by any of his challengers. The mayor was also reassured by poll numbers that highlighted his popularity with a majority of San Franciscans, despite scandalous revelations earlier this year that he has problems with alcohol and had an affair with his appointment secretary, the wife of his then-campaign manager.

As of Tuesday night, only 44,472 ballots had been counted — those cast by absentee prior to Election Day. Of those cast, 77.4 percent were in Newsom’s favor, with Republican candidate Harold Hoogasian trailing far behind in second place with 7 percent of the votes.

The remainder of the votes will be counted in the days and weeks to come through a slow and painstaking process mandated by the state.

San Francisco elections officials learned in September that The City’s electronic voting machines would only be certified for limited use because state testing revealed that ballots marked with lighter inks were at risk of not being counted.

As a result, the 561 machines at the polling sites are not being used to tabulate votes, in accordance with orders from Secretary of State Debra Bowen, who oversees California’s elections. Instead, all of the precinct ballots must be transferred to City Hall to be visually inspected and then fed through a central voting system.

Further slowing down the count, The City’s election workers are required by the state to fill out, or “remake” a new ballot when a San Francisco voter — who is allowed to rank up to three candidates for the same local office — leaves one or more of the slots blank.

According to John Arntz, the head of The City’s elections department, ranked-choice voting in San Francisco has always resulted in ballots being kicked out as “undervotes” when three choices are not ranked. But in the past, election workers have visually inspected such ballots and then put them back through the machine.

This year, because undervotes are also caused by marking the ballot with an inappropriate pen, the state is requiring a remake of the rejected ballot, using the pen provided with the machines — in case the ballot was also kicked out due to the ink, Arntz said.

Arntz said that although the goal is to have 75 percent of the precinct ballots and 65 percent of the absentee ballots counted by Friday, if the polling place “require a lot of remakes, then we won’t make it.”

City election workers will count ballots 24 hours a day and a cumulative tally of results will be reported once a day until all the ballots are counted. By law, election results must be filed within 28 days.

The Examiner first reported the potential disaster in May, shortly after the secretary of state sent a letter to The City’s electronic voting machine provider, Election Systems and Software to say her office would not certify The City’s voting equipment.

Earlier this year, a decision made by the Board of Supervisors resulted in an extension for the ES&S contract instead of an approval of a $12.6 million, four-year contract with Sequoia Voting Systems. At the time, some supervisors said they didn’t want to get locked into a new contract because they had questions about the transparency of the electronic voting machines.

beslinger@examiner.com