Fish consumption was also associated with rapid infant growth between birth and two years of age.
"Contamination by environmental pollutants in fish could provide an explanation for the observed association between high fish intake in pregnancy and increased childhood adiposity," said Leda Chatzi from the University of Crete in Greece.
The research, published in the journal JAMA Pediatrics, studied 26,184 pregnant women and their children in Europe and US.
Of the children studied, 3,476 (15.2 per cent) were overweight or obese at ages four and six.
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The effects were generally greater in girls than in boys. In girls, eating fish more than three times a week was associated with a 31 per cent increased risk of rapid growth early in childhood.
"While fish in general are high in protein and fatty fish provide valuable omega-3 fatty acids, there is now a question as to how much harm might result from accumulation of marine pollutants such as methyl mercury and organic compounds," said Andrew Whitelaw from University of Bristol in UK.