"We save lives but we will not permit illegal activities," Italian Prime Minister Enrico Letta said following a meeting with his Maltese counterpart Joseph Muscat in Valletta.
Muscat slammed the EU for "allowing thousands to cross the Mediterranean and risk their lives".
"We are doing more than our resources permit. We have to send a strong message that we will still save lives but we must combat trafficking," he said, adding that authorities would not stand by and do nothing.
On Saturday, the Italian navy arrested 16 human traffickers aboard a so-called "mother ship" in international waters off Libya.
The fishing boat served as a staging area from which the traffickers dispatched their clients - Syrian migrants seeking asylum or a better life - aboard smaller, often rickety vessels to destinations in southern Europe.
The boat had been under surveillance, including by drones, hi-tech radars, night-vision equipment and submarine, under stepped-up operations launched after two shipwrecks last month claimed some 500 lives.
Rights groups have warned that EU heads of state have so far been focused purely on means of keeping migrants out of fortress Europe, but Italy, Malta and fellow countries on the bloc's southern fringe say they struggle to cope with the boatloads of migrants washing up on their shores.