Survivors on one boat said about 28 people were lost at sea, while three were reported missing from the second after both went down in stormy weather on Saturday, the International Organisation for Migration said.
Both vessels were rickety iron boats believed to have set off from Sfax in Tunisia on Thursday.
Italy's coastguard said it had saved 57 survivors from the two shipwrecks, and recovered the body of a woman and a minor.
It released footage Sunday of the rescues, in which people could be seen carried high on the crests of vast waves, while a coastguard vessel soared and plunged nearby.
While some people tried to climb on to the vessel as it rocked, others wearing black rubber rings clung desperately to one another in a human chain.
Mediators with the IOM believed there were "at least 30 people missing" after speaking to those pulled from the sea, spokesman Flavio Di Giacomo told AFP.
An investigation into the shipwrecks has been opened in Agrigento, on the nearby Italian island of Sicily.
Agrigento's chief of police Emanuele Ricifari said the traffickers would have known bad weather was forecast.
"Whoever allowed them, or forced them, to leave with this sea is an unscrupulous, criminal lunatic," Mr Ricifari told Italian media.
"Rough seas are forecast for the next few days. Let's hope they stop. It's sending them to slaughter with this sea."
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As the stormy weather continued on Sunday, an alpine rescue team and the fire brigade lifted to safety migrants marooned on a rocky part of Lampedusa's coastline.
The Sicilian Alpine rescue service said the 34 migrants had been stuck on the rocks since late Friday, after their boat was tossed on to the rocks by strong wind.
They were provided with food, water, clothes and emergency thermal blankets by the Red Cross, but the coastguard was unable to rescue them by sea because of the high waves.
The rescue service said it had pulled 29 of the 34 people to safety – including six women, two of whom were pregnant – while the fire brigade saved the rest.
The Central Mediterranean migrant crossing route from North Africa to Europe is the world's deadliest.
More than 1,800 people have died attempting it so far this year, Mr Di Giacomo said – almost 900 more than last year.
"The truth is that figure is likely to be much higher. Lots of bodies are being found at sea, suggesting there are many shipwrecks we never hear about," he said.
The number of bodies found has increased in particular on the so-called Tunisian route, which has become increasingly dangerous, Mr Di Flavio said, because of the type of boats used.
Sub-Saharan migrants are being put out to sea by traffickers "in iron boats, which cost less than the usual wooden ones but are utterly unseaworthy. They easily break up and sink", he said.
Migrants also often have the engines stolen from their boats at sea, so that traffickers can re-use them.
Nearly 92,000 people have landed on Italy's shores so far this year, according to the Interior Ministry – more than twice the number in the same period last year.
Authorities said on Sunday the bodies of 10 migrants have been found on a beach in Tunisia, near Sfax.
"Ten bodies have been found over the past 48 hours by coast guard units" north of Sfax in Tunisia's centre-east, the national guard said.
Sfax court spokesman Faouzi Masmoudi told AFP it had been told of the "eight bodies, all apparently sub-Saharan Africans", and investigators were working to identify them.
The dead migrants were "found between Friday and Saturday" during a windstorm that had possibly sunken their boat, Mr Masmoudi said, but noted no reported shipwrecks off Sfax.
They may have embarked from another area along Tunisia's coast, the spokesman said.
The Tunisian Interior Ministry said 901 bodies had been recovered this year by July 20 after maritime accidents in the Mediterranean Sea, and 34,290 others had been rescued or intercepted.
Most of them came from sub-Saharan African countries, it said.
The distance between Sfax and Italy's Lampedusa island is only about 130km.
Almost 90,000 migrants have arrived in Italy this year, according to UN figures.
Most of them embarked from Tunisia or neighbouring Libya, said the UN refugee agency UNHCR.
The central Mediterranean migrant crossing from North Africa to Europe is the world's deadliest, with more than 20,000 fatalities since 2014, according to the International Organisation for Migration.
Crossing attempts have multiplied in March and April after an incendiary speech by Tunisian President Kais Saied who claimed "hordes" of sub-Saharan migrants were causing crime and posing a demographic threat to the mainly Arab country.
Attacks against black African migrants and students have increased across the country since Mr Saied's February remarks, and many migrants have lost jobs and housing.
Since early July, hundreds of migrants have been driven out of Sfax after a Tunisian's death in an altercation with migrants.
At least 1,200 migrants, according to Human Rights Watch, have been taken by Tunisian police during the following days to the desert or perilous areas near the Libyan and Algerian borders.
Humanitarian officials have reported at least 25 deaths of migrants abandoned in the Tunisian-Libyan border area since last month.