Children with the worst reading skills could improve their literacy with daily supplements of fatty acids found in fish, seafood and some algae, researchers claim.

Scientists gave a daily 600mg omega-3 fatty acid pill to children aged seven to nine and found that those whose reading skills were in the lowest fifth of the normal range improved over the four months of the study.

On average, the children in the bottom 20% for literacy boosted their reading age by three weeks more than a control group taking a daily placebo. Those in the lowest 10% for literacy improved their reading age by 1.9 months compared with the placebo group.

The idea that omega-3 supplements can improve brain function in some children is controversial, and the latest study, from researchers at Oxford University, has already drawn criticism. The study was funded by a company called DSM Nutritional Lipids, which makes omega-3 supplements, though the study was performed at Oxford independently.

One contentious point is that the study, involving 74 Oxfordshire schools, looked at reading and behavioural problems in 362 children who were in the lowest third for literacy skills. Analysis on this group of children found no improvements in reading or working memory, and while parents said their children had fewer behavioural problems, their teachers reported no change on these scores.

The positive effects of the pills were seen only in a subgroup of the worst-performing 224 children and for reading only. Again, teachers recorded none of the improved behaviour parents saw, such as less hyperactivity and "so-called opposition-defiant behaviour".

Alex Richardson, who led the study at Oxford's Centre for Evidence-Based Intervention, said the original trial had been designed to look at children in the poorest 20% for reading skills, but children in the bottom third were added to get the right number of participants for the study.

Despite the study's shortcomings, Richardson said the potential improvement in the poorest readers warranted follow-up work to confirm or rule out the effect.

"This is not going to help any child who isn't lacking in these nutrients," she said. "But to bring up the tail-end, that is something that theoretically makes sense. This is such an important group of children in terms of their life chances, and you have to catch them early. It's a cumulative thing.

"Kids who can't read are effectively going to miss out on the rest of their schooling, because if you can't read it is very difficult to access the rest of the curriculum."

Omega-3 fatty acids, such as docosahexaenoic acid (DHA), appear to play a crucial role in brain development by supporting the growth of neurons and their connections to one another. The substance is found naturally in fish oils and some algae, but may be lacking in some people's diets.

However, Michael Crawford, who studied DHA and brain development at Imperial College London, said the substance was vital for healthy brain development of children in the womb.

"Once they are born, the basic architecture of their brain is already defined. You're not going to make an Einstein out of somebody who doesn't have the potential at birth," he said.

But he felt the results warranted further investigation. "You're bound to get a gradation in ability. Some children will be at the top and some at the bottom. The ones at the top you're not going to influence very much, if at all, but the ones at the bottom, the fact that you can make a difference to them is important. It shows there is a potential to help those who are least able."

Crawford said much longer term studies were needed to confirm the extent of any effect of omega-3 on children's brains at school age.

"The problem with all of these studies is that they're really addressing a formed brain, and so they are far too short and underpowered by comparison with any of the sorts of trials we do in clinical medicine. For some reason, the people working with children, on the brain, expect the brain to be manipulated in a period of 16 weeks. It's a fundamental flaw."

Details of the study are published in the journal PloS One.

• This article was amended on 7 September 2012. The original said omega-3 fatty acids are known also as docosahexaenoic acid (DHA). This has been corrected to say omega-3 fatty acids, such as docosahexaenoic acid (DHA).