The decision by a school in Therwil sought to reach a compromise with two male students, aged 14 and 15, and their families, but ended up causing uproar and fierce public debate over the limits of religious freedom.
"We have asked for an expert opinion from our legal service," said Deborah Murith, spokeswoman for the education department in the canton of Basel-Country, where Therwil is located.
The two students informed the school that the Swiss custom of pupils shaking teachers' hands violated their faith if the teacher is a woman.
To avoid approving the de facto discrimination of female teachers, the school decided to exempt the boys from shaking hands with any of their teachers, regardless of sex.
That ruling -- made independently by the school without involvement of the cantonal authorities or municipal officials -- triggered an outcry across Switzerland.
Murith told AFP that the case was "not simple" and that Basel was now trying "to find a balance between religious liberty, the right to education and the legally enshrined equality between men and women."
She said the compromise reached by the school could serve as a "provisional measure", while the legal expert prepares guidance, without specifying when that decision would be made.
The head of the Therwil school system, Christine Akeret, told Swiss media that she plans to abide by the expert ruling, but voiced frustration that she had not previously been given instruction from higher authorities on the matter.
Murith agreed that "there is currently a gap in the current regulation on this subject.
"That is why we have asked for an expert legal opinion," she said.
In an interview with 20 Minuten on Tuesday, Nabil Arab, manager of the foundation running the Basel mosque attended by the two boys - where their father is the Imam, according to reports - defended the boys, saying that they simply want to practise their religion.
Their refusal to shake hands with women was guided by the life of the Prophet, he said, and was actually a sign of respect.
"No woman wants to be a sex object," he told the paper, saying that physical contact with women was a stimuli for young men that could end badly.
"I understand that it may seem strange to many Swiss and I can understand the criticism," Arab added.
Switzerland's population of eight million people includes an estimated 350,000 Muslims.
Previous similar disputes have centred on Muslim parents who demanded that their daughters be exempt from swimming lessons, a case that led to the parents being fined.
Muslim families have however secured victories in court against schools which sought to ban the full face veil.