Michael Gove is coming under pressure to explain what checks his department carried out on a Muslim free school which has been closed since Tuesday.
Al-Madinah, in Derby, cited "health and safety concerns" when it shut last week. It is due to reopen on Monday.
But Labour called on the education secretary to "reassure the public" amid persistent concerns over the school.
The Department for Education was already investigating allegations against the school, a spokesman said.
Free schools - which can be opened by anyone - are state-funded but not overseen by the local authority.
Al-Madinah says it has a "strong Muslim ethos" and when it opened last year claimed to be the first such school in the country for pupils from reception age to 16.
Preliminary findings from an Ofsted inspection into the school gave it the lowest possible rating.
The Department for Education had asked Ofsted to bring their inspection forward. Allegations had been made by parents and staff that pupils at Al-Madinah had been told to follow strict Islamic practices.
Former staff have claimed non-Muslim female teachers came under pressure to wear the hijab head-scarf.
It has also been reported that girls were made to sit at the back of class.
The school denies pupils have been segregated and says its dress code was made clear to anyone wanting to work at the school.
Sources have told the BBC the closure was due to incomplete records of child protection checks being done on all staff.
But ahead of the school re-opening to pupils on Monday, shadow education secretary Stephen Twigg said the situation must be "urgently clarified in order to reassure the public".
In a letter to Mr Gove the Labour MP said: "This is, of course, not the first time that there have been questions surrounding your department's oversight of a free school.
"While I understand that there is an ongoing investigation, the reports concerning this school are of extreme concern to parents and the wider community.
"Given the confusion as to why the school has closed, and that pupils may be returning to the school on Monday, I would ask that these matters be clarified urgently in order to reassure the public."
He called on the department to say what "due diligence" was carried out when the school was approved.
And he asked whether there had been "appropriate vetting" of staff and what oversight ministers had had since it opened.
Interim principal Stuart Wilson closed the school after Ofsted inspectors shared their preliminary findings with him.
"While unfortunate, my decision to close the school related to a short-term health and safety issue that has now been completely resolved and will not reoccur," a statement on the school's website read.
The school "will be open as normal on Monday," Mr Wilson added.
A Department for Education spokesman said: "We were already investigating this school before the allegations became public.
"We discussed the problems with Ofsted and it launched an immediate inspection. We are waiting for Ofsted's final report and considering all legal options."
Mr Twigg also questioned what would happen to children at the school if it did not reopen on Monday or had to close again.