The draft document - which has been leaked to Human Rights Watch and Amnesty International - plans to bar NGOs who do not agree to the code from Italian ports.
This could mean lengthier, and thus, more dangerous journeys for rescued refugees who may be pregnant, torture victims or infants.
It would also require rescue boats to allow police on board and ban them from Libyan territorial waters, communicating with smugglers by phone and using lights to signal their position when under threat of sinking.
"This draft for a code of conduct is a real threat for thousands of people," said Jugent Rettet's Isa Grahn, according to The Independent. Grahn added adding that having police on board a rescue ship would not be feasible.
"Humanitarian work has to be separated from political aims and be protected from political or military intervention," Grahn said.
The leaking of the 11-point plan comes as Italy struggles to gather support from fellow EU countries to take in around 200,000 migrants who are currently in overstretched Italian reception centres.
Over 2,300 migrants have died while attempting to reach Europe this year, many of whom perished while taking the dangerous sea route between Italy and Libya.
The use of sub-standard boats by people smugglers has made the rescue work of humanitarian groups critical. So far this year, humanitarian organisations have picked up over a third of migrants rescued.