PHILADELPHIA — A jury deadlocked Thursday on dozens of charges in a $6 million school fraud case in Philadelphia, while acquitting a charter school founder of witness tampering and five other counts.

Dorothy June Brown, 76, took multiple salaries from four schools she founded, and earned millions more from her consulting company, the indictment charged. Brown made $2 million in one year alone, prosecutors said.

However, three jurors were not convinced that she broke any laws, leading to a 9-3 deadlock on 54 counts against Brown, most of them involving checks that changed hands. The jurors had been working on the case since November, with a two-week holiday break in the midst of deliberations.

“I thought the prosecution did a phenomenal job. I wish the others were able to look at the evidence impartially,” said juror Christine Dick, 55, of Malvern. “They had reasonable doubt. ... That’s their right.”

Federal prosecutors immediately vowed to retry the case, one of several they have pursued involving publicly-funded charter schools.

“We’re very thankful that the jury didn’t find her guilty of anything,” defense lawyer William McSwain said.

The jury previously acquitted co-defendants Michael Slade Jr, who is Brown’s nephew, and Courteney Knight before breaking for the holidays. Two other company officials pleaded guilty before trial.