JERUSALEM — The Israeli military killed six Palestinians on Saturday, three in the West Bank whom it accused of killing a Jewish settler and three in Gaza who it said were crawling along the border wall planning an attack. It was the deadliest day in the conflict in nearly a year.

Salam Fayyad, the Palestinian prime minister, called it “a sad day for Palestinians and their National Authority” and condemned the West Bank operation as an “assassination” and “an attempt to target the state of security and stability that the Palestinian Authority has been able to achieve.”

Maj. Peter Lerner, spokesman for Israel’s Central Command, which controls the West Bank, said that its forces had spent the past two days looking for the killers of the settler, Rabbi Meir Hai, a 45-year-old teacher and father of seven, who was shot dead on Thursday as he drove near his home in the settlement of Shavei Shomron.

The information gathered, he said, led them to three men in the city of Nablus early Saturday. Troops in jeeps descended on their homes and in each case, he said, the suspect was asked to give himself up. None did so, and all were shot dead.

 Ghassan Katib, spokesman for the Palestinian Authority, said Palestinian security had been investigating the killing when the Israelis interfered.

“This is what they do,” he said. “They kill people and then claim they were responsible. Our security forces had begun an investigation into the killing but the Israelis did not coordinate with us.”

Relatives of two of the three men who were in the houses when the raids occurred contended that the men were not armed and that the Israelis shot without warning. In the case of Mr. Tsubakh, relatives said they fled while he remained inside.