The Israeli airstrike targeting Hamas’s military leader, Muhammad Deif, in southern Gaza on Saturday followed weeks of surveillance of a compound used by one of his key lieutenants, Rafa Salameh, according to three senior Israeli defense officials.

The Israeli military and the Shin Bet, Israel’s domestic intelligence agency, said on Sunday afternoon that the strike killed Mr. Salameh, but Mr. Deif’s fate remained unclear. Hamas has denied that either man died in the attack, which killed more than 90 people, according to Gazan officials, in an area designated by Israel as a humanitarian zone.

The strike was authorized after prolonged observation of one of Mr. Salameh’s secret command posts located west of Khan Younis, a city in southern Gaza, according to the three senior Israeli officials.

The villa surrounded by palm trees near the Mediterranean Sea belonged to Mr. Salameh’s family, two of the officials said. Mr. Salameh began spending more time there in recent months after Israeli forces overran many of his other strongholds in Khan Younis, both above and below ground, according to two of the officials. All officials spoke on the condition of anonymity because they were not authorized to speak publicly about the operation’s details.

Mr. Salameh spent much of his time in Hamas’s underground tunnel network, but he also stayed regularly at the villa, along with his family and other militants, to escape the stifling conditions in the tunnels, the officials said.

Officers from an Israeli unit that oversees the identification of high-value targets, staffed by operatives from both military intelligence and the Shin Bet, detected Mr. Salameh’s presence several weeks ago, the officials said. But, they said, Israeli leaders decided to delay any attempts to kill him to see if he would be joined at some point by a bigger target: Mr. Deif.