EU chief Ursula von der Leyen said Wednesday there is "no excuse for hitting a hospital full of civilians" in Gaza, but did not apportion blame for the blast.
The European Commission president told EU lawmakers the "facts need to be established" on the overnight strike on the Gaza hospital which killed at least 200.
Israel and Palestinians accuse each other of the blast, which triggered street protests in the Middle East against Israel.
Von der Leyen said "all those responsible must be held accountable".
European Council President Charles Michel posted on social media that there was "no conceivable reason to strike a facility with innocent civilians and medical staff" and said such an attack "is not in line with international law".
He too called for accountability.
Von der Leyen, who visited Israel last Friday in a show of solidarity, has been criticized by some European Union countries for perceived bias in favor of Israel at the expense of Palestinian civilians.
That prompted Michel to host a summit of EU leaders by videoconference late Tuesday which emphasized that Israel has the right to defend itself following Hamas's bloody assault -- but only in line with its commitments under international humanitarian law.
Hamas on October 7 sent fighters through the Gaza Strip's heavily militarized border, killing more than 1,400 people. They also took nearly 200 hostages.
Israel has been relentlessly bombing Gaza in response, killing over 3,000 people, according to the health ministry in the Hamas-controlled territory.
In her parliamentary address, von der Leyen said Hamas was the underlying reason for the ordeal Palestinians are now going through.
"Hamas are terrorists. And the Palestinian people are also suffering from that terror," she said.
She added that the EU needs to keep supporting the Palestinians, "and there is no contradiction in standing in solidarity with Israel".
"Europe stands with Israel in this dark moment," von der Leyen said, adding that "Israel should act as a democracy, in line with international humanitarian law."
Against 'rules of war'
The EU's top foreign policy official, Josep Borrell, took a sterner view of Israel's reaction, which has resulted in a siege of Gaza and its 2.3 million Palestinians, who are now cut off from water, food, electricity and humanitarian aid.
"Cutting water supplies and food off from civilian populations isn't in line with the rules of law," Borrell told the European Parliament.
"We cannot make the people of Gaza responsible for the terrible actions of Hamas."
The speeches to the parliament, and Tuesday's videoconference EU summit, highlighted divergences within the EU over the Israel-Hamas conflict.
While there has been widespread condemnation of the slaughter by Hamas of Israelis, disagreements over calls to rein in retaliatory strikes on Gaza continue to boil.
