Guidance to schools on how to meet the needs of Muslim pupils refers to a website which claims Israel's founders applauded Nazi racism. It also describes homosexuality as immoral and Darwinism as perverted.
Last week the Muslim Council of Britain published a 72-page report on how schools can accommodate Muslim pupils by providing prayer rooms, having single sex swimming lessons and kitchens providing halal meat.
The National Association of Head Teachers has endorsed the report on its own website.
One site the council recommends is www.harunyahya.com, which it says is useful for exploring "Islamic perspectives on aspects of science and intellectual enquiry". But it includes extremist views.
One section claims: "Historical facts show that the founders of Israel ...
at one time embarked on close co-operation with Nazi Germany reasoning that Nazi pressure would be an excellent motive for European Jews to migrate to Palestine."
Another section says: "Among the most frightening developments is the spread of homosexuality ... Around the world their activities show their opposition to religious faith and their antagonism to religious values."
It adds: "Tolerating homosexuality as a normal way of life is an important sign of the period before the Last Day."
Darwinism is described as "the world's most perverted faith".
Tahir Alam, the council's education committee chair, said: "If there is anything objectionable, we will be happy to review it."
Mick Brookes, the NAHT general secretary, said he was considering taking off the endorsement.