Dairy Crest, one of Britain's biggest dairy firms, said there was scientific evidence to back its claim that "increasing the intake of omega-3 may enhance learning and concentration in some children".
The firm said the Advertising Standards Authority (ASA) had told it to ditch the claim from two press adverts for its St Ivel Advance omega-3 milk, following complaints from the public.
The ruling, set to be published by the ASA later this week, deals a blow to the food industry as it looks to push health claims for omega-3.
Britain's Joint Health Claims Initiative has approved a generic health claim that foods containing omega-3 benefit heart health, but not learning ability or concentration.
Still, Dairy Crest has built St Ivel Advance around the slogan "clever milk".
The product has done well since its launch in May 2005, reaching annual retail sales of £13m after its first year and helping the firm move further into higher margin, added value markets.
Lord Robert Winston, a high profile scientist who took part in the Dairy Crest adverts, joined the company in criticising the ASA.
"I have carefully reviewed the full text of well over 200 scientific publications, published in peer-reviewed journals, which address the possible merits and dosage of omega-3 in adults and children in various situations and conditions," said Winston.
"There is a very strong case for encouraging parents to give their children more omega 3," he said, adding milk was a good means of doing this.
Dairy Crest said St Ivel Advance contained the same omega-3 fatty acids as those used in the so-called Oxford/Durham study, which found omega-3 could indeed aid children's concentration.
It is thought, however, that St Ivel Advance milk contains significantly less omega-3 than the amount given to children in the study.
The ASA refused to comment on the ruling until it is officially published later this week.
Dairy Crest said it had already changed its adverts for St Ivel Advance milk to comply with the ASA decision. It added that the watchdog had acknowledged the science was still emerging on the issue and offered to revisit its ruling after new studies had been published.