A Reform rabbi has challenged the entry rules used by some Orthodox schools because they take into account synagogue attendance only on Saturday mornings and not Friday nights.
Rabbi Mark Goldsmith, of London's North-Western Reform Synagogue, said that the entry policy used by JFS was "galling".
But the school said that its entry criteria had been devised simply for administrative ease and not for any religious reasons.
This latest bone of contention illustrates the complications of applying the new faith-based tests that Jewish schools were forced to introduce after the courts ruled that they could no longer select pupils simply on the basis of Jewish parentage.
For entry next year to JFS and two of London's other Orthodox schools, Yavneh College and King Solomon High, applicants must have a certificate of religious practice (CRP), countersigned by a rabbi or another Jewish organisational representative.
To get priority, applicants must score three points. If they have attended synagogue on Shabbat mornings eight times since May, they score three: six times, two points: and three times, one point.
They can also score a point each for receiving Jewish education for the past two years and if they or their parents have volunteered in a Jewish organisation.
Under last year's hastily drawn-up rules, attendance on High Holy Days and other services counted towards entry qualification, but the rules have been amended for 2011.
Rabbi Goldsmith said: "What has been very galling is that to meet JFS's criteria, only attendance on Shabbat morning 'counts'."
His own synagogue's Friday night Kabbalat Shabbat, he said, attracted "up to 200 together every week to welcome Shabbat in song and prayer - but these attendances are irrelevant as far as JFS is concerned and so we have had to disappoint parents who have come weekly with their children, but not in the morning."
He went on: "I hope that the JFS Jewish participation criteria next year will recognise that Shabbat begins at sundown on Friday and is not only Saturday morning."
But Michael Glass, chairman of JFS, explained that before finalising the application form for next September, "JFS, Yavneh and King Solomon consulted representatives of the United Synagogue, Federation, Sephardi, Masorti, Refom and Liberal movements. We pursued the above policy specifically to avoid accusations of bias to any particular religious denomination."
He believed that the general view was that "more people came on Shabbat morning and all parties wanted a simple administrative process. I don't recall Friday night being requested by any communal organisation."
The new cross-communal Jewish Community Secondary School operates a different policy: applicants either have to belong to synagogues, or attend a synagogue four times since May, or have been in Jewish education and participated in a Jewish organisation.