The NGOs said a regulation to stop sailing near Libya would be difficult to enforce in international waters.
Italy, France and Germany held a working dinner on Sunday to prepare the ground for a six-point plan to address the biggest migrant phenomenon since World War II, to be submitted to the bloc at a meeting on Thursday in Talinn.
Top of the list was a code to regulate operations in the sea off Libya where the Italian coast guard, European border patrol forces and non-governmental organisations (NGOs) save migrants attempting the perilous crossing.
Up to a dozen private aid boats have been patrolling off the coast of Libya since 2015.
They performed 26 percent of the rescues carried out in 2016, rising to 35 percent so far this year, according to the Italian coastguard.
They have been accused of acting as a magnet by sailing close to the Libyan coast.
In reply, they insist that not doing so would risk lives, as smugglers are putting migrants out to sea in increasingly unseaworthy vessels with little fuel or water.
The Maltese organisation MOAS told AFP Tuesday it was "very perplexed" by the code-of-conduct proposal as all rescues in the Mediterranean are already automatically coordinated by a command centre in Rome.
Ruben Neugebauer, spokesman of the German NGO Sea-Watch, was equally as baffled, saying: "there is already a code of conduct in place -- it is called international maritime law".
SOS Mediterranee, which was recently awarded a UNESCO peace prize for its efforts to save lives, said it was "surprised that the first response by European leaders to a major humanitarian crisis is for a code of conduct for the NGOs".
Italian coast guard head Vincenzo Melone gave the aid groups his backing in May during an audition with a parliamentary committee in Rome looking into whether the NGOs were encouraging people trafficking from Libya.
"We are facing a tragedy of incredible dimensions... (but) the solution is not at sea," he said. Since 2014, the coast guard has coordinated the rescue of over 590,000 migrants, while over 14,000 have died or are feared drowned.
The coast guard holds meetings in Rome with NGOs to facilitate coordination. The next one is scheduled for July 13.
"There's no anarchy among the aid groups, the anarchy is in Libya, a country without any state structures worthy of the name, where large-scale human trafficking is proliferating," said vice president of SOS Mediterranee Sophie Beau.
It is the "EU which really needs a code of conduct", Oscar Camps, head of Spain's Proactiva Open Arms, said on Twitter.
He pointed to a campaign against the NGOs which shifted attention from crisis-hit Libya or the reasons behind the mass migratory movement -- people fleeing war or hunger -- by slinging mud at the rescuers.
"'You're a pull factor, you are in cahoots with the traffickers, you are financed by the mafias, you are the taxis of the sea, we are going to close the port'," he said, quoting the critics.
"Are we really the problem?" he asked.
Italian media reports said the code of conduct would forbid NGOs from sailing near the Libyan waters or communicating with smugglers -- including using any form of lights that could attract traffickers.
The NGOs said a regulation to stop sailing near Libya would be difficult to enforce in international waters, and pointed out they use searchlights to look for men, women and children who risk drowning in the dark.
The code may also include an obligation to have a police officer on board the aid boats. The NGOs have said that would go against their humanitarian principles.
"But if the police want to come on their own boats, they are very welcome. We need more boats" saving lives, he said.