Leifer, 56, is accused of sexually abusing Melbourne sisters Nicole Meyer, Dassi Erlich and Elly Sapper when she was head of religion and principal of the the Adass Israel School in the city's eastern suburbs between 2003 and 2007.
The mother of eight has pleaded not guilty to 27 charges and has faced trial in the Victorian County Court.
The jury returned to court on Tuesday morning after 14 hours of deliberations over several days, to ask for advice on a deadlock situation.
"At this point in deliberations, the jury seems unlikely to reach an unanimous decision on all charges," they said in a note to Judge Mark Gamble.
"Can you please offer direction on a deadlock? Is it possible to use a majority verdict on charges?"
It's not clear if the question related to all or just some of the charges.
Judge Gamble said he was not satisfied they were unable to reach a unanimous decision, and urged them to return to the jury room to try to resolve their differences through calm and rational examination of the evidence.
Experience has shown juries can often agree if given more time, he said.
The jury of six men and six women have resumed deliberations.
Prosecutor Justin Lewis argued Leifer had a tendency to have a sexual interest in girls when they were teenage students at the school and when those same girls were student teachers.
Mr Lewis said the tendency was to engage in sexual activities with them and to take advantage of their vulnerability, ignorance in sexual maters and her position of authority in order to do so.
Her barrister, Ian Hill KC, argued the lengthy delay between the alleged offending and the trial, which began in February, was a disadvantage to the defence and to jurors.
He attacked the credibility of the sisters, including accusing one of telling "blatant lies" in her evidence.
"Truth and reliability were lost in false accounts," he said.
"Perhaps even at times hardened into false imaginations and false memories of false realities."
Two charges were dropped during the trial because evidence revealed alleged offending pre-dated relevant legislation.