The charity was appearing for the Government, which is facing a legal challenge from Sue Axon, who is divorced with five children, over the right of under-16s to have an abortion without their parents' consent or knowledge.
Ms Axon launched a legal challenge to the government guidelines after they were introduced in July 2004, citing her fear that one of her daughters could fall pregnant and have an abortion without discussing it with her first.
She has admitted that her daughters are not entirely behind her demand for a judicial review of the guidelines, and on the third day of the hearing, it emerged that Ms Axon's eldest daughter, Joy, 16, is nearly five months' pregnant.
Ms Axon, from Manchester, is said to believe the pregnancy reinforces her concern that the guidelines act to encourage children to have underage sex. But the Department of Health, responsible for drawing them up, insist they are vital in the battle to reduce teenage pregnancy rates and improve sexual health.
Backing the DoH's guidelines, Nathalie Lieven, for the FPA, said that "parents were no longer necessarily the best people to advise a child", and that the traditional "paternalistic approach" that assumed they were ran contrary to social changes in Europe over the last 20 years.
Confidentiality was the "single most important factor" for teenagers seeking sexual health advice, she said. "There is no doubt whatsoever that a child has a right to confidentiality," she said, adding that "a parents' rights cannot override a child's rights", particularly as it could not always be guaranteed that a parent would act in their child's best interests.
"They may be highly loving parents, or have extremely strict views on under-age sex, or extremely strict views on abortion, or teenagers having babies," she said.
Ms Axon's lawyers have argued that the guidelines are "keeping parents in the dark", and preventing them from being able to fulfil their parental responsibilities.
But the Government pointed out that children are entirely at liberty to tell their parents if they choose to do so and Ms Lieven argued that where a child was reluctant to tell a parent, blame lay with the parent who had failed "to establish a relationship of trust with the child".
Philip Havers QC, appearing for Ms Axon, said the public would find the FPA view's on the rights of parents "astonishing".
"I would hazard a guess that the vast majority of people in this country would support the proposition that, in the overwhelming majority of cases, the best judges of a child's welfare are his or her parents", he said.
"I would hazard a guess that the vast majority of people in this country would be astonished to be told that view was out of date and out of step."
Mr Justice Silber, who heard the case, will announce whether he will grant a judicial review at a later date.
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