While Israel defended the attacks on Tuesday as being justified, Qatar said Israel was treacherous and engaged in "state terrorism".
Qatari Prime Minister Sheikh Mohammed bin Abdulrahman al-Thani said the airstrikes threatened to derail the peace talks Qatar has been mediating between Hamas and Israel.
US President Donald Trump said he considered hitting Hamas was a worthy goal, but he felt badly that the attack took place in the Gulf Arab state, which is a major non-NATO ally of Washington and where the Palestinian Islamist group has long had its political base.
It has acted as a mediator alongside Egypt in talks on a ceasefire in the almost two-year-old war in the Gaza Strip.
White House spokeswoman Karoline Leavitt said the attack "does not advance Israel or America's goals" and the United States felt badly about the location of the attack.
The attack drew condemnation from Saudi Arabia, Egypt, the United Arab Emirates and the European Union, and risks derailing Gaza ceasefire talks and Trump's push to achieve a negotiated end to the nearly two-year-old conflict.
Qatar is a security partner of the US and host to al-Udeid Air Base, the largest US military facility in the Middle East. It has acted as a mediator alongside Egypt in talks between Israel and Hamas for a ceasefire in Gaza, which appears to be increasingly elusive.
Hamas said five of its members had been killed in the attack, including the son of Hamas's exiled Gaza chief and top negotiator Khalil al-Hayya. It said Israel had failed in what Hamas called an attempt to assassinate the group's ceasefire negotiation team.
The Trump administration received warning of the attack from the US military just before it took place, Trump said in a statement on social media. He did not say if it was Israel that notified the US military.
"Unilaterally bombing inside Qatar, a Sovereign Nation and close Ally of the United States, that is working very hard and bravely taking risks with us to broker Peace, does not advance Israel or America's goals," Trump wrote.
"However, eliminating Hamas, who have profited off the misery of those living in Gaza, is a worthy goal."
Hamas political bureau member Suhail al-Hindi told Al Jazeera TV the group's top leadership had survived the Israeli attack. The airstrike followed Israel warning Palestinians to leave Gaza City, an area once home to about a million people, as it tries to destroy what is left of Hamas, which has been decimated by Israel's military since October 2023.
Trump said he directed his envoy Steve Witkoff to warn Qatar the attack was coming but Qatar contradicted those comments, saying that reports that it got a heads-up before the attack were false and the phone call from a US official came when blasts were already being heard in the Qatari capital, Doha.
"Qatar reserves the right to respond to this blatant attack and will take all necessary measures to respond," al-Thani told reporters. Israel killed one member of Qatar's internal security forces in its attack and injured others, Qatar said.
Trump assured the emir of Qatar in a phone call after the attack that "such a thing will not happen again on their soil". The US president also spoke with Israeli Prime Minister Benjamin Netanyahu.
Israeli officials told Reuters the strike was aimed at top Hamas leaders including Hayya. Israel is still gathering information on the strike and is yet to determine whether any Hamas officials or leaders were killed, a person briefed on the matter told Reuters.
Two US officials, speaking to Reuters on condition of anonymity, said the US military had been notified by Israel shortly before the strike but there was no co-ordination with or approval from Washington.
The airstrike took place shortly after Hamas' armed wing, the Qassam Brigades, claimed responsibility for a shooting on Monday that killed six people at a bus stop on the outskirts of Jerusalem.
Netanyahu said the attack was "entirely justified" and was ordered after the Jerusalem attack and the deaths of four Israeli soldiers in Gaza.
"The days are over when terror leaders can enjoy immunity of any kind," Netanyahu said in a televised address. "I won't allow that kind of immunity to exist."
The Israeli operation drew strong negative reactions around the world.
The European Union called it a breach of international law and the United Arab Emirates, which normalised relations with Israel under the Abraham Accords in 2020, called it "blatant and cowardly".
Pope Leo expressed unusually forceful concern about the consequences of Israel's strike in Qatar.
"The entire situation is very serious," he said.
UN Secretary-General Antonio Guterres condemned the attack and said Qatar had been playing a very positive role in seeking a ceasefire in Gaza and the release of hostages held by Hamas.
with AP
