"I am appalled by these new tragedies at sea and I express my condolences to the victims and their families," she said in a statement on Sunday, adding that she would meet with Italian Interior Minister Angelino Alfano on Wednesday in Brussels to discuss the latest developments.
The Italian navy said on Monday that six bodies were recovered following a shipwreck off the Libyan coast on Sunday night, the third tragedy to hit immigrants attempting the perilous journey across the Mediterranean this weekend.
"Last night, north of the Libyan coast, with weather conditions deteriorating, a fishing boat carrying a large number of migrants capsized," the navy said in a statement. Rescue workers managed to pull 364 migrants from the sea.
Earlier in the day, an Italian navy ship had approached a boat in difficulty and found 18 dead along with 73 survivors on board.
"I also thank the Italian authorities for the huge efforts put in place to assist and rescue thousands of migrants over the last days," Mogherini said.
Italy's navy, coast guard and merchant marine have rescued more than 3,500 people since Friday in the stretch of the Mediterranean between Sicily and the Libyan and Tunisian coasts.
Faced with the new crisis, Malmström again urged member states "to provide assistance to Mediterranean countries facing increased migratory and asylum pressure, in particular by resettling people from refugees' camps outside the EU".
Many of the migrants making the risky and often deadly journeys are refugees from Eritrea, Somalia and Syria, but there are also many arriving from across Asia and sub-Saharan Africa.
More than 100,000 migrants have landed in Italy so far this year, according to the UN refugee agency UNHCR — far higher than the previous record of some 60,000 who arrived in 2011 at the height of the turmoil triggered by the Arab Spring revolutions.
Figures released at the end of July showed some 93,000 migrants had been rescued since the start of 2014.
The European Commission has said the refusal of member states to respond more favourably to asylum requests was fuelling the crisis.
It has suggested member states agree on creating humanitarian visas or deal with the requests at consulates in refugee camps and at points along migrants' journeys.