The 11-point code is aimed at regulating operations in the sea where the Italian coast guard, European border patrol forces and nine NGOs currently operate vessels which rescue stranded migrants.
Italy's Interior Minister Marco Minniti wants the code, which would include the NGOs agreeing to allow an armed officer on board, to take immediate effect, arguing that it is crucial “for the security of the country”.
"Over 40 percent of rescued migrants arrive in Italy on ships operated by NGOs," he was quoted by Ansa as saying.
The aim of having an officer on board would also be to root out human traffickers hiding among migrants.
Other rules include a ban on making calls or firing flares that might alert people smugglers to sending boats crammed with migrants out to sea.
But some of the NGOs, including Spain's Proactiva Open Arms, have refused to sign the code. Germany's Sea Watch argued that the code would have the opposite effect of saving human lives.
"In light of the more than 2,000 deaths at sea this year, what is needed is not more rules, but greater rescue capacity," the organisation said.
Almost 94,000 people have been brought to safety in Italy so far this year, according to the Italian interior ministry, an increase of more than five percent compared to the same period last year.
More than 2,370 people have died since January attempting the perilous Mediterranean crossing, mostly on unseaworthy and overcrowded boats, the UN refugee agency says.