A far-right Israeli minister confronted the detained flotilla activists, mocking their aid initiative and accusing them of supporting "terrorism" in a video that was circulating on Friday.
In Italy, workers and students took to the streets after the country's largest unions called for a one-day general strike in solidarity with the Palestinians and the flotilla.
Hundreds of trains were cancelled or delayed, as were several domestic flights, and many private and public schools were closed.
The last boat in the Global Sumud Flotilla, the Marinette, had been trailing behind the rest of the vessels and was still sailing on to the Palestinian territory in the early hours of Friday, a day after the Israeli navy stormed 41 other boats and detained the activists, saying they would be deported.
A livestream from the Marinette showed the moment Israeli troops boarded the vessel.
The flotilla, which was carrying a symbolic amount of humanitarian aid to Gaza, was the largest attempt so far to try and break Israel's blockade of the Palestinian territory.
Israel's interceptions started on Wednesday night and continued through Thursday as boat by boat was stopped off Gaza's shore and the activists - including Greta Thunberg, Nelson Mandela's grandson Mandla Mandela and several European MPs - were detained.
Israeli authorities had warned the Marinette would be stopped, too, if it continued on its journey.
The interceptions of the flotilla boats and the arrest of the activists sparked demonstrations across continents, from Latin America to Asia.
Tens of thousands of people took to the streets again late Thursday and on Friday in Italy, Spain, France, Switzerland and other countries to protest the arrest of the activists and to demand an end to the war in Gaza.
In Israel's southern port of Ashdod, the country's far-right national security minister, Itamar Ben-Gvir, was filmed visiting the site where activists were being processed ahead of their deportations.
He accused the flotilla participants - who come from more than 40 countries - of supporting "terrorism", and aboard one of the seized boats, mocked the activists' aid initiative.
In the footage, the activists are seen sitting cross-legged on the floor while Ben-Kvir stands and delivers his accusations, with one person heard shouting back "Free Palestine".
By Friday afternoon, at least four Italian citizens were deported, Israel's foreign ministry posted on X.
"Israel is keen to end this procedure as quickly as possible," the ministry said.
Hundreds of police officers were deployed to Ashdod as Israel on Thursday marked Yom Kippur, one of the holiest days of the Jewish calendar, to handle the detentions of the activists.
Israel had repeatedly criticised the flotilla and accused some members of links to Hamas, while providing little evidence. Activists have strongly rejected the accusations.
One of the flotilla boats that had been sailing at the back of the convoy - and turned back to avoid an Israeli interception - returned to Cyprus's Larnaca port on Thursday evening with 21 people aboard.
Already, another flotilla of boats with dozens of activists have set sail last week from Italy across the Mediterranean Sea.
The nine-vessel group made of the Freedom Flotilla Coalition and the Thousand Madleens group was still days away from the Palestinian strip, according to the boats' tracker.
