The plea was made on Monday, after some 629 refugees, including minors, children and pregnant women, on a rescue ship were refused entry and left waiting in international waters between the two countries.
Italy’s new Interior Minister and leader of the far-right League Party, Matteo Salvini, had closed Italian ports a day earlier and refused to let in the humanitarian ship, Aquarius, operated by SOS Mediterranee and Doctors without Borders. He had also sent a letter to the island-state of Malta, south of Italy, threatening to close all the Italian ports if the Maltese government refused to take the ship, Presstv Reported.
European Commission spokesman Margaritis Schinas described the situation as an urgent “humanitarian imperative," and called on Italian and Maltese authorities to provide care to the stranded refugees on the ship.
"For the (European) Commission, there is first and foremost a humanitarian imperative. We are talking about people. Over 600 people including unaccompanied minors. The priority of both the Italian and Maltese authorities should be ensuring these people receive the care they need," he said at a news conference.
"We call on all involved to contribute to a swift resolution so that the people on board the Aquarius vessel may be safely disembarked as soon as possible," Schinas added.
The Commission noted that international law obliged the country coordinating the search and rescue operation - in this case Italy - to pick the port to which the vessel should go.
In a statement, the United Nations High Commission for Refugees (UNHCR) also "appealed to concerned governments to allow the immediate disembarkation of hundreds of people stranded in the Mediterranean since Saturday."
The refugee agency’s special envoy for migrants in the Mediterranean, Vincent Cochetel, stressed that "people are in distress, are running out of provisions and need help quickly."
"Broader issues such as who has responsibility and how these responsibilities can best be shared between States should be looked at later," he said in the statement.
Aquarius is currently between Malta and Sicily, waiting for a secure port.
“Saving lives at sea is a duty, but transforming Italy into an enormous refugee camp is not,” Salvini said on his Facebook page. “Italy is done bowing its head and obeying. This time there’s someone saying no.”
Maltese Prime Minister Joseph Muscat said he had told his Italian counterpart, Giuseppe Conte, that his country would not accept the ship, ignoring calls from Rome.
“We are concerned at Italy authorities’ directions given to Aquarius on high seas. They manifestly go against international rules, and risk creating a dangerous situation for all those involved,” Muscat said on Twitter.
Europe has launched a string of schemes to tackle its worst refugee crisis since World War II. The continent has been hit since 2014 by an unprecedented influx of refugees who are fleeing conflict-ridden zones in North Africa and the Middle East, in particular Syria.
Many blame major European powers for the mass exodus, saying their interference has led to a surge in conflicts and terrorism in troubled regions, forcing people to flee their homes.
Over the past five years, more than 600,000 refugees have reached Italy by risking their lives in the sea. Some 500,000 of them are still staying in the country.
According to United Nations figures, at least 500 people have died this year as they were trying to cross the central Mediterranean. Some 2,853 also lost their lives last year.