It said another 15 operations would be underway before nightfall.
The United Nations estimates that 32,750 people have arrived in Europe by sea so far this year, despite the risky winter weather.
Frontex has two programs at sea.
Between Thursday and Friday, 73 migrants were rescued from five boats by Spanish ships. The Triton program enlists member states to provide assets for search and rescue operations.
"The professional conduct and tireless efforts of our crew are to thank for the many lives saved today". Italian prosecutors have suggested the non-government affiliated groups have links to traffickers, a claim the groups have strongly denied. Find us on Facebook too!
No charges have been filed, but Zuccaro told CNN he would seek to sequester the charity ships if he found just cause to do so.
Tens of thousands of migrants, mostly from sub-Saharan African countries, try to reach the shores of Spain and Italy by boat each year.
Frontex has been contacted for comment.
The NGOs, on the other hand, have not minced words. "We know exactly what will happen if we are not out there". It is not known how many died before they were sighted. "We are where we're needed, what's the European Union doing meanwhile?" "I will never forget this day", tweeted Chris Catrambone, founder of Maltese NGO Moas.
A Somali migrant carries her 12-day-old baby on board a rigid-hulled inflatable boat.
"Many more people could have died in a day like this if we arrived a few hours later. Probably, many more", MSF said on Twitter.
The Libyan coast guard rescued a further 23 migrants of various African nationalities off the coast of Tripoli, he added.
Jugend Rette, a German NGO involved in the rescuing of migrants, told AFP that good spring weather has led to increased numbers of people attempting the unsafe crossing in recent days, Deutsche Welle reports. "We need help by #MRCC" the Jugend Rettet tweeted.
In all, Italy's coast guard coordinated about 20 separate rescues on Friday. The weekend is set to be the latest marker in the ongoing humanitarian crisis.
The voice that is often missing from the discussion is often that of the migrants themselves.
So far rescuers have pulled 453 people to safety, but were forced to suspend the operation overnight with their rescue vessel the Phoenix running at full capacity. The boat was due to arrive in the port city of Argostoli in the early evening.