The Milwaukee Journal Sentinel reported its analysis found the total reported for the city could be tens of thousands of voters higher than the number that actually cast ballots.
For example, the city reported that there were 78,801 ballots cast for the major-party candidates for attorney general.
But adding the votes cast for the two Republican and two Democratic candidates gave a total of only 40,971, the newspaper said. That would indicate 37,830 voters did not cast ballots in that race, which would be highly unlikely for one of the most hotly contested elections on Tuesday's ballot.
The Sentinel reported that the exact same number of voters were counted at polling places across the city — which it said is a "red flag" that the results were bogus. Four of Milwaukee's wards came in with turnouts inexplicably higher than 100 percent – the highest had a turnout of 145.4 percent.
The city didn't meet a deadline of 4 p.m. Wednesday to turn in its polling lists and voter information to the Milwaukee County Election Commission.
Kevin Kennedy, executive director of the state Elections Board, said it appeared that a computer programming problem resulted in the inaccurate totals.
He said the city should re-examine the totals using polling-place records and make sure no outcome was affected.
The figure must be corrected, he said.
"I need to know, by law, how many voters there were," Kennedy said.
Susan Edman, executive director of the City Election Commission, said the newspaper's questions about the gap in totals alerted her to the problem. She said she suspected a computer programming error was to blame.
She also said she was confident no individual races were affected. City and county election officials planned to meet Thursday to decide how the results should be verified.
Meanwhile, Waukesha County Clerk Kathy Nickolaus said some returns from the city of Waukesha inexplicably had data recorded in the wrong column, which momentarily skewed results in the 97th District Assembly race.
Computer monitors at the clerk's office late Tuesday briefly showed Christine Lufter winning her Republican primary, as county officials scrambled to correct flawed returns from the city of Waukesha. Final results later showed Lufter losing to Bill Kramer by a significant margin.
"The best thing to do is go back to paper," Nickolaus said. "And that's exactly what we did."
Lufter said Wednesday that she would not likely challenge the outcome, although she was still trying to sort out what happened.
"There was obviously a huge problem," she said.
Meanwhile, the state Elections Board planned to tell county clerks to black out voters' bank account numbers before releasing them in open record requests.
Election officials are required by law to record a number with statements such as utility bills voters use as proof of residency to register at the polls.
The state recently added bank statements to the list of proof. But bank account numbers aren't confidential like driver's license numbers, birth dates and Social Security numbers. That means someone could obtain the bank numbers through an open records request, creating a risk of identity theft.