They revealed that seven of the products they intercepted contained added sugar, according to trade magazine The Grocer.
Chi, Foco, Go Coco, Tropical Sun, Suncrest, Yaco and Pearl Royal were the culprits, the National Food Crime Unit said.
A FSA spokeswoman said the retailers had been asked to make sure consumers can be "confident they are purchasing authentic, correctly marketed coconut water".
They added that none of the goods carried any health risks, but 400 tonnes of coconut water was seized, the magazine reports.
Sugar: The dangers
The Government recommends a maximum of 30g of added sugar a day for adults, which is roughly seven sugar cubes.
Consuming any more than this set amount can lead to obesity, diabetes and tooth decay. Some studies have also shown a link to dementia.
And scientists have warned sugar could be as addictive as cocaine, as they found it to have a similar effect on the brain as the powerful illegal drug.
The medical community has been embroiled in a bitter row in recent years over the true dangers of sugar, as some claim it to be worse than salt.
Experts are increasingly worried about consumption of sugar across the world, particularly among children.
Average sugar intake is nearly three times the recommended limit, according to Public Health England figures.
Researchers are constantly discovering sugar in seemingly guilt-free snacks and savoury foods, including salad dressings and bread.
What did the firms say?
Jonathan Newman, founder of Chi, said: "We take the matter extremely seriously and have, since then, put in many checks in place."
He blamed factories in Asia, which they use to make their products, for "trying to maintain artificially low prices" because of soaring demand.
Ross Currie, managing director of Freedom Brands, which owns Go Coco, said the results "could not be proven". He added: "This batch never entered the UK market."
A spokesperson for Tropical Sun said: "We have not sold a single drop of tainted coconut water."
The other firms had not responded to The Grocer's request for comment at the time of publishing this article.