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, although hitting Hamas was a worthy goal.
Qatar is a key US security partner 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 on a ceasefire in the almost two-year-old war in the Gaza Strip.
Leavitt told a briefing that Trump's administration was notified by the Pentagon that Israel was attacking Hamas in Qatar "just before" and US President Donald Trump spoke to Israeli Prime Minister Benjamin Netanyahu after it.
Leavitt also said the US military was notified "just before the attack" but did not respond when asked by whom.
"Unilaterally bombing inside Qatar - a sovereign nation and close ally of the United States that is working very hard in bravely taking risks with us to broker peace - does not advance Israel or America's goals," she said.
"However, eliminating Hamas, who have profited off the misery of those living in Gaza, is a worthy goal."
Qatar condemned the action as "cowardly" and called it a flagrant violation of international law.
The assault is likely to deal a serious, if not fatal, blow to the ceasefire efforts, especially since negotiations have often taken place in Qatar.
Hamas said five of its members had been killed in the attack in Doha, including the son of Hamas' exiled Gaza Strip 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.
Earlier, Hamas political bureau member Suhail al-Hindi told Qatar's al-Jazeera TV that the group's top leadership had survived the Israeli attack.
Israeli officials told reporters 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 source briefed on the matter told Reuters.
Earlier, several blasts were heard in Doha and plumes of black smoke were seen billowing from the city's Legtifya petrol station.
Next door to the petrol station is a small residential compound that has been guarded by Qatar's emiri guard 24 hours a day since the beginning of the Gaza Strip conflict.
The United Arab Emirates, which normalised relations with Israel under the Abraham Accords in 2020, called the Israeli attack on Doha "blatant and cowardly".
Regional power Saudi Arabia denounced what it called a "brutal Israeli aggression" against Qatar's sovereignty.
The European Union said the air strike breached international law and Qatar's territorial integrity, warning against risks of a further escalation of violence in the region.
"We express full solidarity with the authorities and the people of Qatar, a strategic partner of the EU," a representative for EU foreign policy chief Kaja Kallas said in a post on X.
"Any escalation of the war in Gaza must be avoided - it is in no one's interest. We will continue to support all efforts towards a ceasefire in Gaza."
with AP
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