But the headmaster did not consult parents - a move being seen by critics as further evidence of families being denied a say over their children's sexual wellbeing.
Rising numbers of clinics at secondary schools already offer condoms and the morning-after pill. They have the power to do so without seeking parental permission.
Hugh McKinney, chairman of the National Family Campaign, said: "Schools need to be reminded that sexual relations with children under 16 is a criminal offence."
School matron Heidi Thomson, a registered nurse who supplies the tests to pupils, said: "If girls ask for pregnancy tests they are already having sex and need help and advice."
But family campaigner Mr McKinney added: "Schools should not be in involved in issues like pregnancy testing. This is a subject for medical practitioners and parents to discuss, not for schools to provide."
Asked about the scheme, a mother who has a son and a daughter at the school said: "Personally, I would hope my children would be able to talk to me first.
In a statement, Milton Keynes Council said: "While we applaud the initiative and recognise the special circumstances in which the school operates, we feel that it might have been more appropriate to have undertaken a little more consultation prior to the introduction of these tests."
In April last year, the Daily Mail told how 14-year-old Melissa Smith of Mansfield had an abortion arranged by her school without her mother's knowledge.
Last week, mother of five Susan Axon, 51, of Wythenshawe, Greater Manchester, began a High Court battle to overcome a Government policy which allows girls under 16 to terminate pregnancies without their parents knowing.
Britain has Europe's highest rate of teenage pregnancies. It is five times the rate of the Netherlands, three times that of France and twice that of Germany.
Although the Government has pledged to halve it by 2010, latest figures show that the number of under-18s becoming pregnant in England and Wales rose to 42,173 in 2003, from 41,868 the year before.
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