Updated 2.30pm with EP president's office reaction
European Parliament president Roberta Metsola was greeted at MCAST by a small group of students holding papers calling her an "enabler of genocide".
In a Facebook post, NGO Moviment Graffitti uploaded photos showing the tudents holding the papers.
Graffitti said they accused Metsola of "having blood on her hands after exchanging handshakes with Israeli war criminals and standing with an occupying state while it was indiscriminately brutalising Palestinians".
A Moviment Graffitti spokesperson told Times of Malta nine students were part of the protest.
In the past weeks, Metsola has been criticised over her support of Israel following her October 13 visit to the country shortly after Hamas gunmen stormed into Israel and killed 1,400 people, including many civilians.
She also led MEPs and parliament staff in a solemn ceremony in front of the European Parliament to show solidarity with all those targeted in the attacks.
Metsola however, has repeatedly insisted that both she and the European Parliament are advocating for a two-state solution to bring an end to the hostility.
'We are pushing for de-escalation'
Reacting to the protest, a spokesperson said Metsola had always made it clear the European Parliament is on the side of peace and has always made a distinction between Hamas and the aspirations of Palestinians.
"We have been working tirelessly towards ensuring safe humanitarian corridors in Gaza, respect for international and humanitarian law, doing all we can to avoid civilian casualties and destruction of civilian infrastructure, get aid through and free the hostages taken by Hamas on October 7th," it said.
"We have called for a pause in hostilities precisely to allow this to happen, to push for de-escalation in the region and lasting stability in the region."
It said Metsola would continue to meet with and speak to representatives of all nations in the region to push these aims forward.
Israel has since hit 11,000-plus targets in Gaza. Although many nations backed Israel's right to strike back at Hamas, as the civilian toll has mounted, so too has criticism of Israeli tactics.
The Hamas-run Gaza health ministry says more than 9,000 people have died in Israeli bombardments, mostly women and children. Entire neighbourhoods have been destroyed.
During a protest by the Palestinian community in Malta last month, placards showing Metsola and the word "complicit" were also held up at the protest.
Even Prime Minister Robert Abela criticised a "prominent politician" for using the conflict in Gaza to promote themselves and appear in international media.
Although he did not mention EP President Roberta Metsola by name, government sources had said the message "was clear".
On Saturday, a protest will be held by 'Youths for Palestine' in solidarity with Gaza. The march will take place outside Parliament in Valletta starting at 3pm. Moviment Graffitti will also be taking part.