JFS head Jonathan Miller has said that the Ofsted report which raised concerns about safety and behaviour "is not an accurate reflection of the school we know".
But he has promised to address the issues raised by the inspection service.
In the report, published this week, inspectors said that a minority of JFS students "do not demonstrate consistently positive attitudes towards learning across all subjects and teachers".
They added: "The school's behaviour policy is not applied in the same way by all staff. Sanctions are not given in a fair and consistent manner and are being used too frequently by some teachers."
They also found that "not all students have good attendance".
I have already written to parents as there is a partnership
While they acknowledged students' high academic performance, they noted: "The small number of lower ability students, disabled students or those who have special educational needs, and students who are eligible for the additional pupil premium funding, do not achieve as well as other students."
Ofsted has downgraded the school from outstanding to one requiring improvement, cutting its rating from grade one to grade three out of four.
The unannounced inspection took place in July after Ofsted received complaints from parents. It declined to give details.
Mr Miller said that many of the points raised by inspectors had already been highlighted by the school. He said: "My job is not to complain about the report. My job is to respond to the areas for improvement. Many of them were already areas we had identified in our own self-evaluations, and had plans in place to deal with."
Mr Miller said he knew complaints had been made and was able to find clues as to what they were within the report. "I think the small number of complaints seem to be from a small number of parents who, we regret, were unhappy with the outcome of an issue at the school."
He would not elaborate on the nature of the issue.
When it was last inspected in 2009, it was judged "outstanding" in all categories. The largest Jewish school in Europe with more than 2,000 students, it continues to perform well academically and had a record 16 Oxbridge offers this summer. Mr Miller, who has been head for six years, noted that the inspections had been carried out before exam results had been announced.
He said the inspection had come as a shock. "The question is whether, against the background of complaints, you get a completely objective result. A lot of pupils had already broken up - the whole of years 11 and 13 - so it was absolutely not representative of the school."
He said he would work to ensure there was "clarity about our expectations - on the part of students, parents and staff. I gave an assembly this week about the report. I want students to know two things: if there are elements of their behaviour which are good, then there will be a reward.
"But on those occasions when that small number of students misbehaves, then they must be clear that we have standards and there are consequences.
"Our attendance is in the mid-90s per cent. We want 100 per cent attendance, and that is something we are addressing. I have already written to parents on the subject because there is a partnership there. We need to ensure that parents support us by making their children come to school."
Mr Miller said that, since the results were announced, he had received support from across the community.
"There were immediately expressions of surprise and astonishment," he said. "That is the feedback I am getting in the overwhelming majority of cases from colleagues, parents, governors, people at shul."
