Speaking in Qatar while receiving condolences, Haniyeh said "the interests of the Palestinian people are placed above everything" when asked if the strike would affect the talks on a truce and hostage release.
"We are seeking to reach a deal but the occupation is still procrastinating and evading a response to the demands," he told Reuters.
Israeli forces carried out Wednesday's attack without authorisation from top commanders or senior leaders, Israeli media said on Thursday, raising fears among families of hostages it would derail efforts to secure their release from Gaza.
"I can only hope this won't affect the negotiation. I hope it won't make Hamas put harder conditions on the deal," said Ofri Bibas Levy, whose brother Yarden Bibas was taken captive with his wife and two small children during the Hamas-led attack on southern Israel on Oct. 7.
Israel's government has faced rising pressure from families of the 133 Israeli hostages still believed to be held in the Hamas-ruled Gaza Strip, although talks mediated by the U.S., Egypt and Qatar have yet to secure a deal.
"The key to any agreement with the occupation starts with a permanent ceasefire and our top priority in the ongoing negotiation process is the unconditional return of the displaced and the complete withdrawal of forces from the Gaza Strip," Hamas spokesperson Abdel-Latif al-Qanoua said in a statement.
"Without that, an agreement will not happen," he added.
Israeli Prime Minister Benjamin Netanyahu's government has faced mounting criticism from Israel's main ally, the United States, over the conduct of its military campaign and the chain of command in pursuing its objectives.
This has been prompted by the rising number of Palestinian civilians killed and stoked most recently by a strike that killed foreign and Palestinian aid workers in Gaza.
STRIKES
Israel's Walla news agency reported that neither Netanyahu nor Defence Minister Yoav Gallant had been told in advance of Wednesday's strike on Haniyeh's sons, which was coordinated by the Israeli military and the Shin Bet intelligence service.
Quoting senior Israeli officials, it reported that the three adult sons, Amir, Mohammad and Hazem Haniyeh, had been targeted as fighters and not because they were the sons of Hamas's political leader.
The Israeli military did not comment on reports that four of Haniyeh's grandchildren had also been killed.
The military declined to comment on Walla and other reports. No comment was available from the prime minister's office.
Haniyeh, 61, told Reuters his sons were not active Hamas fighters. "These claims are lies to justify this crime and massacre," he said.
"They were going on Eid day visiting relatives," he added in a reference to Eid al-Fitr celebrating the end of the Muslim holy month of Ramadan.
The conservative Israel Hayom daily quoted unnamed military officials saying the strike was carried out in accordance with procedure but said there was a question about whether hitting such a sensitive target should have been carried out without first consulting superiors.
The left-wing Haaretz newspaper, a relentless critic of Netanyahu and his government, called the killings and last week's assassination of senior Iranian officials in the Iranian embassy in Damascus "proactive acts of aggression, designed to thwart any chance of a hostage deal".
Two officers were dismissed last Friday for misjudgement and breaches of operating procedures in a strike on an aid convoy in Gaza that killed seven aid workers.
Global calls for a ceasefire have been growing as the war has entered its seventh month but there has been little sign of progress in the talks.
Hamas is demanding an end to the Israeli offensive, a withdrawal of Israeli forces and permission for Gaza's displaced Palestinians to return to their homes.
Israel wants to secure the return of the hostages but says it will not end the war until Hamas is destroyed as a military force, and that it is still planning to assault the southern city of Rafah, where more than a million civilians have taken refuge.
