Nearly one in two licensed fertility clinics have "anomalies" in their records, a regulator's audit has revealed.
Checks by the Human Fertilisation and Embryology Authority show "anomalies" in records kept by 51 of 109 licensed clinics.
Detail emerged today in a ruling by the most senior family court judge in England and Wales.
Sir James Munby, President of the Family Division of the High Court, described the outcome of the audit as "alarming" and spoke of "administrative incompetence".
The judge said the creation, storage and implantation of embryos was controlled by "complex" legislation - the 1990 Human Fertilisation and Embryology Act.
Provisions dealt with the question of who, legally, were the parents of a child.
He said there were "fundamental prerequisites" to the "acquisition of parenthood" by the partner of a woman receiving treatment.
Written consent had to be given in writing before treatment - by the woman and her partner, and the woman and her partner had to be given "adequate information" and offered counselling.
Another family court judge had analysed a case two years ago in which "lamentable shortcomings" had been revealed at one clinic.
Sir James said records checks at all licensed clinics had been organised in the wake of that case.
Results showed that forms were "absent" from clinics' records, forms had been completed or dated after treatment had started and forms had been incorrectly completed.
Sir James said audit results had triggered family court litigation - and he had been asked to analyse a number of cases which raised the question of whether "valid consents" had been given.
He said a number of couples had asked him to make a "declaration of parentage".
The judge had analysed issues raised at a hearing in July - and published a ruling today.
"This judgment relates to a number of cases where much joy but also, sadly, much misery has been caused by the medical brilliance, unhappily allied with the administrative incompetence, of various fertility clinics," said Sir James.
"The cases I have before me are, there is every reason to fear, only the small tip of a much larger problem."
He added: "The Human Fertilisation and Embryology Authority required all 109 licensed clinics to carry out an audit of their records. The alarming outcome was the discovery that no fewer than 51 clinics (46%) had discovered 'anomalies' in their records."
Sir James said the picture was "alarming and shocking" and "deeply troubling".
"The picture revealed is one of what I do not shrink from describing as widespread incompetence across the sector on a scale which must raise questions as to the adequacy if not of the Human Fertilisation and Embryology Authority's regulation then of the extent of its regulatory powers," he added.
"That the incompetence to which I refer is ... administrative rather than medical is only slight consolation, given the profound implications of the parenthood which in far too many cases has been thrown into doubt."
He said there was an "imperative need" for all clinics to comply "meticulously and at all times" with the authority's guidance and directions.