The country has been on the frontline of migrant arrivals from across the Mediterranean, and in recent years has struggled to provide accommodation for the thousands of newcomers.
"We have saved many lives but we cannot accept rule-breaking. We need to speed up deportations," Foreign Minister Angelino Alfano, the country's former interior minister, said in an interview with La Stampa daily.
He was "working to tie up agreements which will reduce arrivals and prevent departures" from the coast of North Africa, he said after a record 181,000 people were rescued from the Mediterranean and brought to safety in Italy in 2016.
Clashes broke out over living conditions in the Cona migrant centre in the Veneto region following the death of a 25-year-old woman of a blood clot on Monday. An investigation has been opened into the death of the woman, named by Italian media as Ivory Coast native Sandrine Bakayoko, amid reports that workers at the centre waited several hours before calling an ambulance.
During the protests, asylum seekers set fire to furniture and objects inside the facility, and cut electricity. Italian media reported that 25 staff members had to barricade themselves inside a room overnight, though no injuries were reported.
A parliamentary delegation had visited the centre last November, where over 500 migrants live in the former military base.
The MPs presented a report to the Interior Ministry at the time denouncing "serious structural deficiencies", Repubblica reported.
One member of the delegation, Nicola Fratoianni, condemned the poor living conditions including lack of water and light, and and said the centre had been a "ticking timebomb".
There had been protests in early 2016, when a small group protested about poor hygiene and sanitary conditions. And a peaceful sit-in was held in August, to protest long waiting times for asylum decisions.
Over 1,400 people were housed in the space originally intended for just 15.
On Wednesday, 100 people were transferred from the Cona centre to Bologna, where they were destined for other facilities.
They were met by a small group of Italian demonstrators holding banners reading: "Solidarity with those who revolt".
The violence at the centre was condemned by politicians from all of Italy's main parties, with far-right leader Matteo Salvini taking advantage of the incident to call for support.
"When I'm in government, there will be mass expulsions, centre closures, and the navy ships will send people back after saving them," the head of the Northern League wrote on Facebook. "Enough! 2017 will be the year of sending them back."
MP Marietta Tidei of the Democratic Party responded to Salvini's comments, saying that while the violence at the centre should be condemned, Italians should reject "the reprehensible exploitation of Matteo Salvini, always ready to fuel a dangerous climate of migrant hatred".
There were also renewed calls from organizations which work with migrants to restructure the reception centre system, because the so-called 'maxi-centres' are unmanageable.
According to the latest government figures, 175,485 migrants currently live on Italian territory, spread out between reception centres, 'hotspots', and migrant and refugee centres.
A total of 14,669 of those live in temporary accommodation centres (CPA), of which there are seven in Italy, including the one in Cona.
These centres are only designed for migrants to live in for a short period, however the average time spent there has increased throughout 2016, particularly since neighbouring France, Austria and Switzerland closed their Italian borders, making it impossible for many migrants to make their planned journeys on to northern Europe.
Three countries 'key'
Interior Minister Marco Minniti said at least one "Centre for Identification and Expulsion" (CIE) will be opened in every region of Italy in the coming weeks, where those who have had their asylum request rejected will be held before deportation.
Returning migrants is a costly, time-consuming process that requires bilateral agreements with the countries of origin. Alfano said three countries were "key" to tackling the biggest migrant crisis since World War II: Libya, Niger and Tunisia.
The EU believes just over half the migrants arriving in Italy travel first through Niger and last month it offered Niamey 610 million euros ($635 million) to curb transit towards Europe.
Alfano said Italy was "close to sealing an agreement" with the West African country, while Minniti spent Tuesday in Tunisia for talks on "renewing" a repatriation agreement between Rome and Tunis.
Italy's police chief Franco Gabrielli vowed at the weekend to deport more migrants who have no right to be in the country following the shooting in Milan of the suspected attacker behind the Berlin Christmas market tragedy.
Tunisian Anis Amri had arrived in Italy by boat in 2011. He spent time in a detention centre and several prisons in Sicily for violent behaviour after Italy tried but failed to deport him back to Tunisia, and was finally ordered to leave the country in 2015.
His return to Italy - where he was shot dead - after the Berlin attack raised fears he was attempting to contact jihadist plotters here.
By Ella Ide and Catherine Edwards