Sicily-based prosecutor Carmelo Zuccaro sparked a row last week after claims in La Stampa daily that some aid groups battling Europe's worst migrant crisis since World War II may be in league with people smugglers.
"I am 100 percent in agreement with prosecutor Zuccaro as he asked a real question... Those who become indignant at the drop of a hat are hypocrites," Alfano told reporters in the Sicilian town of Taormina.
The city will host the G7 summit at the end of next month.
Zuccaro doubled down on his La Stampa comments Thursday when he said he regretted being unable to investigate his claim that some NGOs were "perhaps" financed by traffickers and were potentially seeking to "destabilise the Italian economy."
Prime Minister Paolo Gentiloni said Saturday that "if magistrates have usable and credible information (regarding Zuccaro's claim), the government will certainly not stand in the way" of its being investigated.
"That said, for us, the activities of charitable organisations is precious and welcome," Gentiloni said in Brussels, where he was attending an EU summit to discuss Britain's withdrawal from the European Union.
Justice Minister Andrea Orlando has called on Zuccaro to present evidence if he has any while Interior Minister Marco Minniti cautioned against making "generalisations" on the thorny migrant issue.
Around a dozen privately-financed charities including established groups such as Doctors without Borders and Save the Children have joined newer groups such as Malta-based MOAS to coordinate rescues with Italy's coastguard.
The charities have firmly rejected Zuccaro's allegation as a baseless slur, insisting their mission is simply to save lives in the absence of EU governments acting effectively to do so.
Zuccaro said in his La Stampa interview he had "proof" of his allegation some NGOs were in league with traffickers.
His claims come as the methods used by migrants and traffickers to cross the Mediterranean have shifted markedly over the past few years.
Until 2014, smugglers relied on large "motherships" to bring migrants to Italian waters, before transferring them to smaller boats that would bring them to the coast.
But the launch of Italy's extensive Mare Nostrum patrols made large ships much more conspicuous, prompting smugglers to pack migrants onto smaller vessels and rubber dinghies.
Departures increased after Italy halted Mare Nostrum at the end of 2014, saying it could not bear the cost of the programme alone.
Currently, the aid groups supplement the current European military presence -- the anti-smuggling operation Sophia, border control agency Frontex and Italian navy and coastguard.
Their job has got harder as smugglers put dozens and sometimes hundreds of people on dinghies or rickety wooden vessels, often without a satellite phone that could be used to call for help.
Over 1,000 migrants are feared to have died in waters between Libya and Italy so far this year, according to the UN's refugee agency. Nearly 37,000 have been rescued and brought to Italy.
In contrast, the populist Five Star Movement -- which last week alleged that NGOs were offering a "taxi" service to migrants -- and the anti-immigrant Northern League saluted Zuccaro for his comments.
Aid groups have also been urged by some anti-immigrant parties to leave migrants to drown to dissuade others from attempting the crossing.