Nearly 3,000 votes effectively disappeared during the machine recount of Florida’s midterm races, according to election records, calling into question whether officials relied on a flawed process to settle the outcome of three statewide contests.

With extremely narrow gaps separating candidates in the still-undeclared races for both governor and United States Senate, the results of the machine recount of all votes cast in the Nov. 6 election, posted by the Florida secretary of state’s office, showed 900 fewer votes than those reported in the original statewide tally.

The discrepancy was expected to grow by an additional 2,000 votes when updated numbers from Broward County, whose results initially were disqualified because they came in two minutes late, are added to the statewide results on Sunday.

None of the discrepancies would be enough to affect the outcome of the three statewide and three local elections that are still waiting for a winner to be called. But they come as at least three Florida counties — two of them Democratic strongholds whose results could be decisive — have reported problems counting their shares of the more than 8.1 million ballots cast across the state.

In one of the most serious cases, Palm Beach County found “dozens of precincts missing a significant number” of votes during the machine recount, according to the supervisor of elections, Susan Bucher, causing the county to conclude that entire boxes of ballots may not have been counted.

Ms. Bucher blamed an overheated and outdated ballot-scanning machine. But the manufacturer of the high-speed scanner used in Palm Beach said its technicians had witnessed Palm Beach County elections workers, apparently worried that one of the machines was running too fast, jam a paper clip into the scanner’s “enter” button in an effort to slow it down. That, in turn, caused a short circuit that cut off the power, a company spokeswoman said.

So serious were the problems that the county was unable to complete its machine recount on time and its results were not included in the state vote totals on Thursday. Whatever discrepancies it had were not part of the nearly 3,000 votes missing in the machine recount total.

Two power failures in Hillsborough County appear to have caused the recount there to come up nearly 850 votes short of the original tally, local officials said. Rather than submit numbers he knew were incorrect, the elections supervisor said he had scrapped the results.

Miami-Dade County was short about 500 votes, state records show.

Elections experts say that although the difference in vote tallies were relatively small in proportion to the number of votes cast, they represent the loss of legally cast votes and highlight flaws in election law reforms put in place in the wake of the state’s disastrous 2000 presidential election vote count.

State officials said some fluctuations in vote counts are normal. “It is expected that as each set of results are due, the numbers will fluctuate some,” said Sarah W. Revell, a spokeswoman for the Florida secretary of state. “It is not indicative of a problem.”

But while some levels of error in vote tallies, known as variance, occur in most recounts, the loss of nearly 3,000 votes is substantial, several experts on the vote-counting process said.

Florida is scheduled to certify results in the races for governor, Senate and agriculture commissioner on Nov. 20. All three races went to an automatic machine recount last week when the results of an initial tally, reported Nov. 10, showed that their margins fell within 0.5 percentage points. After that, a manual recount was ordered in the Senate and agriculture races when the machine recount showed the margins were less than 0.25 percentage points.

It was in the total results reported from the initial tally on Nov. 10 and the results of the machine recount reported on Saturday that the discrepancies in the total number of votes showed up.

The difference in Broward County was 0.29 percent — higher than the margin between the candidates in both the Senate and agriculture commissioner’s races.

“This is a big deal,” said E. John Sebes, founder of Open Source Election Technology, a nonprofit group in San Francisco that promotes accuracy and security in the vote-counting process. “If you have an election margin of 0.21 percent and a variance of 0.12 percent, the variance of your machine count is half the margin you are trying to correct. That’s kooky.”

It wasn’t only missing votes that raised questions about Florida’s election results. The vote count in heavily Democratic Broward County increased by about 80,000 in the four days after the election, possibly because of mail-in, provisional, overseas and military ballots that come in late and were legally counted after Election Day.

But no other counties showed were identified publicly with such a high number of additional ballots registered after the election, and Broward County’s election supervisor, Brenda C. Snipes, offered few explanations.

Noteworthy to outside election experts were the variances in vote tallies, which effectively meant that thousands of votes weren’t counted.

“If I were a campaign, I’d be yelling and screaming,” said Charles Stewart III, director of the Election Data and Science Lab at the Massachusetts Institute of Technology. “I’d want a hand recount of every single ballot.”

Mr. Stewart said there was no substantial harm done if, as appears to be the case, the correct winner was eventually chosen. “I don’t see any evidence the wrong person was declared the winner,” he said. “But if four to five thousand votes didn’t show up, you think, ‘Hmm, I wonder if that’s one of my ballots.’”

Florida changed its recount statute after the 2000 presidential race. The state’s much-maligned punch-card ballot system was retired, and there is now a 15-page document to describe how disputed ballots should be judged.

But the deadlines for meeting the Nov. 20 certification date are still tight, and don’t offer sufficient time for a more thorough review of tight races, including the possibility of examining all ballots by hand, several experts said.

“Florida tried to clean up its act, and this was the first time it was put to the test,” Mr. Stewart said. “I would hope wiser heads in Florida would take a deep breath and say, ‘O.K., we can do better next time.’”

Some local officials in Florida recognized problems as they undertook the machine recount over the past several days. When the machine recount in Hillsborough County came up 846 votes short of the number originally counted, Craig Latimer, the supervisor of elections, said he tossed the results of the machine recount and let the original tally stand.

“Even though we achieved 99.84 percent success in our recount effort, we are not willing to accept that votes go unreported,” Mr. Latimer said in a statement. He said that the recount process required sorting through more than a million pages of ballots.

He stressed that the margin between the candidates had remained constant, even with the missing votes.

The county had not yet conducted a full review to determine whether a power failure during the count or human error was to blame, he said.

In Broward County, an elections official said that 2,000 ballots had been “co-mingled.”

“We did not correctly handle the ballots,” said Joseph D’Alessandro, head of operations there. “We are going to look into that and see what took place.”

Miami-Dade did not return a request for comment.

In Palm Beach, the elections supervisor, Ms. Bucher, said the count was eventually reconciled, but it did not matter: The county missed the deadline to submit its numbers. She blamed the machine used, which she said overheated, and she disputed the manufacturer’s account that no technicians had been called about what she said had been an overheating problem.

“We have no reports of an overheating system that night,” said Kay Stimson, vice president of government affairs for Dominion Voting, one of two companies certified to provide the ballot counting machines in Florida. “The motors shipped there to be on hand are still in the box.”

Teresa Paulsen, spokeswoman for ES & S, the other company, said machine recounts depend on the same number of ballots being entered into the system. Some ballots could have been torn or damaged after the election, which could have cause a different result in the recount, she said.

The machines that were used in the recount are normally used to count absentee ballots. The machines at the precincts used on election night are more accurate, Mr. Stewart said.

Michael McDonald, an elections expert at the University of Florida, said sometimes the errors revealed after recounts actually occurred on the first go-round, for example, in cases where precincts may initially have been counted twice.

“A close recount is going to expose all the warts you have in election system,” he said. “It’s an election administrator’s prayer to not have a close election, so those warts are not revealed.”

Barry Richard, a lawyer for Andrew Gillum, the Democratic candidate for governor who came within 33,000 votes after the machine recount in his race against the former Republican congressman, Ron DeSantis, said the amount of lost votes would not have been enough for his candidate to win.

“What it tells us is, these machines are not perfect,” Mr. Richard said. “We know people are not perfect. We particularly know that people in Broward are not perfect.”

Glenn Thrush in Tallahassee, Fla., and Jane Smith in Riviera Beach, Fla., contributed reporting.

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