Tabulators work on recounting presidential ballots in Dane County, Wisc.

MILWAUKEE—A recount of presidential election ballots began in the state of Wisconsin Thursday, with election officials and poll workers expected to work overtime to meet a 12-day deadline by which results have to be verified.

In a warehouse south of downtown Milwaukee, at least 60 county employees, election workers and representatives of the presidential campaigns gathered as the recount process began at 9 a.m. Ballots, which had been locked in secure locations, were transported over to the warehouse escorted by police.

“The City of Milwaukee will be working 6 days a week to get this done,” said Joe Czarnezki, the Milwaukee County Clerk.

The recount was triggered by a petition filed by Green Party candidate Jill Stein, who, advised by prominent computer scientists, alleged that vote counting machines used to tabulate ballots in the presidential election could have been tampered with or hacked. Ms. Stein had pushed for ballots to be counted by hand, but lost a lawsuit in Wisconsin that would have mandated all 72 counties use that method.

A similar recount is expected to begin Friday in Michigan and a hearing in Pennsylvania state court is for Monday over whether a recount can begin there. The three states had long voted Democratic but flipped to Mr. Trump this year, helping to seal his victory.

Officials in all three states have said that they have found no evidence of tampering and expect results to be the same.

In Wisconsin, county clerks have discretion over what method to use in recounting ballots. In Milwaukee, election workers will feed ballots through the same machines used to count the ballots the first time around, following a similar process conducted on Election Night.

Forty-nine other counties, including Dane County where the state capital of Madison is located, will be doing the recount by hand.

“The recount in Wisconsin begins today as a critical first step towards restoring faith in our voting system,” said Ms. Stein in a statement Thursday. “We urge county election administrators to use hand recounts, cited as the gold standard in Monday’s court decision, and not simply push a button that would repeat whatever problems may have occurred in the original tally.”

In Milwaukee, county officials began the morning by testing vote counting machines, ensuring all of them worked. One was malfunctioning and a technician had to be brought in to fix it. Election workers then began verifying absentee ballots and will later arrange ballots in stacks according to presidential candidate.

Staff in Wisconsin will have to go through each ballot, by hand or by running it through the machine, to ensure that the ballot was cast for the candidate that was initially thought.

Representatives from the campaigns of Democratic nominee Hillary Clinton and president-election Donald Trump were present. The Clinton representatives declined to comment. Mrs. Clinton’s campaign had said previously that it would back Ms. Stein’s recount efforts and would be on the ground to monitor the recount process, though it doesn’t expect the result to change.

Mr. Trump, however, has continued to dismiss charges that his victory was illegitimate and claimed, without evidence, that he would have won the popular vote as well as the electoral college had millions of people not voted “illegally.”

Dozens of election observers from the Trump campaign attended training sessions before the recount where they were briefed on irregularities to look out for. In particular, they will ensure that absentee ballots have two signatures on them, one from the voter and one from a witness, and that every ballot be initialed by a poll worker.

Orville Seymer, an observer with the Trump campaign in Milwaukee, said he believed it was “almost impossible” for the recount to change the election result and that many were frustrated with the process.

“People are tired,” he said. “It is Christmas season, people should be out shopping, celebrating, but instead we are here.”

Write to Shibani Mahtani at