The lawsuit, filed by activist lawyers ClientEarth and chemicals campaigners ChemSec, says the European Chemicals Agency (ECHA) breached transparency laws by refusing to disclose the names of facilities producing 356 potentially dangerous chemicals.
ECHA is Europe's agency for evaluating and restricting more than 30,000 substances that currently face little regulatory oversight, many of them a potential risk to human health.
Companies wanting to sell chemicals must register them with ECHA, including details on toxicity, which the agency will publish on its website.
A dispute has erupted over whether ECHA can also publish names of manufacturers - a move chemicals companies say will endanger their commercial confidentiality and was not intended when the control laws were agreed in 2007.
ECHA told Reuters last week it had decided to publish company names only in the case of firms that are suppliers of hazardous substances, but that they could request confidentiality. The move will be voluntary for producers of non-hazardous chemicals.
The agency, based in Helsinki, was not immediately available on Monday to comment on the court action.
ClientEarth lawyer Vito Buonsante said he had "exhausted all avenues" to get transparency on toxic chemicals, and ChemSec said legal action at the EU's General Court was now necessary.
"Knowing who is producing dangerous substances, and the level of exposure, is vital to safeguard the public," said ChemSec campaigner Jerker Ligthart.
"These chemicals are present in many consumer products, from detergents and paints to computers and toys, and often in high concentrations," he added. "Commercial interests should not be given precedence over people's health."
Chemicals industry group Cefic opposes publication of company names, saying it might help overseas rivals compile a detailed picture of the European chemicals market.
It might also help customers switch chemicals suppliers to cut out the middle-man and it could reveal changes of strategy or innovation with new products.
(EurActiv with Reuters.)