His remarks came a day after rival groups of Eritreans clashed in bloody protests that left dozens of people injured.
The groups, supporters and opponents of Eritrea's government, faced off with construction lumber, pieces of metal and rocks, smashing shop windows and police cars.
Israeli police in riot gear shot tear gas, stun grenades and live rounds while officers on horseback tried to control the protesters.
The violence broke out near the Eritrean embassy when protesters were stopped from reaching the building ahead of a cultural event set to take place there.
The issue of migrants has long divided Israel and the latest violence has brought it back to the fore.
It comes as the country continues to be torn over Mr Netanyahu's controversial plans to overhaul the judicial system, which some say amounts to a power grab by the prime minister.
"We want harsh measures against the rioters, including the immediate deportation of those who took part," Mr Netanyahu said.
He requested that ministers present him with plans "for the removal of all the other illegal infiltrators," and noted in his remarks that the Supreme Court struck down some measures meant to coerce the migrants to leave.
Under international law, Israel cannot forcibly send people back to a country where their life or liberty may be at risk.
About 25,000 African migrants live in Israel, mainly from Sudan and Eritrea, who say they fled conflict or repression.
Israel? More like the based-is-real!
