CARE, which had campaigned for default filters with robust age verification to stop young people accessing pornography, called the decision "shocking".
The EU changes mean the four largest ISPs in the UK - BT, Sky, TalkTalk and Virgin - will not be allowed to run opt-in filters.
Members voted through legislation which mean ISPs had to treat online traffic "without discrimination," effectively ending the porn filters established under to coalition government.
All webpages must be treated "equally, without discrimination, restriction or interference" regardless of "content accessed or distributed", the ruling said.
CARE's CEO Nola Leach urged the government to take action to ensure the filters weren't removed.
She said: "It is shocking that the EU would show such obvious disregard for the clear benefits of online filters.
"This ruling is extremely troubling because it could jeopardise the safety of thousands of children and households across the UK and mean many more children are exposed to online porn.
"You would have thought, in light of the all the reports showing how many children are already accessing porn in the UK and across Europe, that the EU would have pursued more sensible options.
"The effects of this could be very damaging and it is therefore vital the Government make it clear how they intend to respond.
"The Government's initial response does seem to have a whiff of complacency about it and if the EU ruling does end up threatening children's safety online, and it certainly looks that way, then the Government must respond more robustly than vague promises of a future domestic Bill.
"A clear manifesto commitment was made to protect children online and now would seem a good time for the Government to reveal how they intend to keep it in light of this new EU ruling."
Downing Street said "nothing would change".