Voting booths are seen though glass past library patrons as people cast their votes inside the Enoch Pratt Free Library in Baltimore on April 26. (Patrick Semansky/AP)

Maryland state elections officials have ordered that the results of Baltimore’s recent primary election be decertified after watchdogs and candidates complained that the process was flawed.

State Elections Administrator Linda H. Lamone said the number of ballots cast in the April 26 contest was hundreds more than the number of voters who checked in at polling places. The state also identified 80 provisional ballots that hadn’t been considered.

“It’s important every ballot is counted,” Lamone said.

It doesn’t appear likely that the investigation will change the results of Baltimore’s Democratic mayoral primary, where Senate Majority Leader Catherine Pugh finished more than 2,000 votes ahead of Sheila Dixon, a former mayor of the city.

Statewide election results in the U.S. Senate and presidential primary cannot be certified until the problems in Baltimore are resolved.

Discrepancies between the number of ballots and voters aren’t unusual and were also spotted in five other counties this cycle, Lamone said. But she said the size of the discrepancy, and Baltimore’s inability to resolve it, prompted an unusual state intervention.

It is possible that election judges prematurely scanned provisional ballots, which are available to people who show up at precincts but whose names do not appear on registered voting lists, she said.

Next week, officials will conduct a precinct-by-precinct review of documents to find out if that was the case, but they will not recount votes. Nikki Charlson, Lamone’s deputy, says that provisional ballots that should not have been counted cannot be removed from vote totals, meaning illegal votes could stand.

Under Maryland’s new paper-based voting system, provisional ballots can be sent through the same scanner as other ballots. Because people casting those ballots are not found on voter rolls, they would not be counted as having checked in at a polling place.

Armstead B.C. Jones, director of the Baltimore City Board of Elections, accused the state of bungling the rollout of new machines and failing to adequately prepare local officials running the elections. He said confusion over provisional ballots was fueled by constant changes in procedures mandated by the state, including after election judges were trained.

“The State Board of Elections basically gives the directions to the local boards and leaves them out to dry,” Jones said. “They want to put me under the bus to try to blame me.”

Election watchdogs had cited numerous problems with voting in the city on April 26, including some polling stations opening late, campaign staffers working as election judges, and shortages of ballots and ballpoint pens at some centers.

They had called on Gov. Larry Hogan (R) to investigate and welcomed the intervention of the State Board of Elections — which operates independently of the governor’s office.

“There was no integrity in the whole election process,” said J. Wyndal Gordon, a Baltimore lawyer who says he is not affiliated with any candidate. “I’m glad the state government is investigating these matters a little closer so we can have a real election where we can have a true victor and not have the specter linger that the presumed winner wasn’t the actual winner.”

Pugh’s office declined to comment on the latest complication with election results. On Wednesday, Dixon said she would not pursue a recount but would continue to seeking answers about problems with the election.

“Additional review is a good thing to ensuring the integrity of the election process,” said Martha McKenna, a spokeswoman for Dixon.