JERUSALEM — At their West Bank home last month, 15-year-old Mohammed al-Tamimi’s family said it was a miracle the teenager was alive after being shot in the head with a rubber-coated metal bullet by an Israeli soldier.

Mohammed himself only talked a little, still struggling with his injury. A deep scar ran along his head, which sagged on the left hand side where part of the skull had been removed. He had spent nearly a week in a coma, they said.

But on Monday night, a top Israeli military chief for the Palestinian territories slammed his story as “fake news,” despite medical records and testimony from witnesses that backed up the family's version of events.

The teen, who had been arrested in a night raid in the early hours of the morning as he was still awaiting surgery to have his skull bone put back in, had admitted under questioning that he had been injured when he had fallen off his bike, Maj. Gen. Yoav Mordechai posted on Facebook. Mordechai is the head of the Israeli military authority responsible for government policy in the Palestinian territories, known as COGAT.

That fact exposed that “culture of lies and incitement continues among the children and adults of the Tamimi family,” he said.

It is just the latest twist in a long-running saga between the well-known Palestinian activist family and Israeli authorities. Mohammed’s 17-year-old cousin Ahed is on trial for charges including assaulting a soldier, after a video went viral of her lashing out at two soldiers in the yard of her home.

With Ahed turning into a Palestinian cause celebre, the family says that Israeli authorities are desperate to silence them. At the first hearing of Ahed’s trial earlier this month, the military judge ruled that it should be held in secret, despite her lawyer’s protestations. Part of her defense is that the soldiers were part of a group that had shot Mohammed just moments earlier.

“They want to do anything in their power to discredit not only Mohammed, but also the family,” said Mohammed’s uncle Attalah Tamimi. He said that the boy was scared, not in a fit medical state to be questioned, and said he had fallen off his bike because he was afraid that he would be detained if he admitted he was shot during a demonstration. He is on anti-epilepsy medication to prevent seizures, he said.

“He must be the first Palestinian teenager that the Israeli army believes when he denies he is involved in clashes,” said Jonathan Pollak, an activist with the campaign to free Ahed. He described the turn of events as “preposterous.”

The extended Tamimi clan dominates the West Bank village of Nabi Saleh, where they hold weekly protests against Israeli occupation and the neighboring Israeli settlement, which they say has stolen their land and water spring. Israeli critics paint them as provocateurs and even actors, with a subcommittee of the parliament launching an investigation in 2015 into whether the family was real or actors.

A spokesman for the Israeli military declined to comment whether there was a record of anyone having been shot with a rubber bullet in Nabi Saleh on Dec. 15, the day in question. A medical report provided by the family from a hospital in Ramallah says that Mohammed was admitted with a bullet injury. The hospital confirmed that it was genuine.

The bullet had entered his head, but there was no exit wound, the report said. It described him as drowsy and bleeding “profusely.” After an urgent brain scan, a “metallic bullet [was] noted in the left temporal lobe,” it said.

“This is not a case of he says, she says,” said Pollak, who said he was about 30 meters away when the incident happened and helped Mohammed to a hospital. “The boy was shot.”

Rights groups said that Mordechai's statement is shocking. A statement from COGAT later reiterated that the post under the heading “The truth about Mohammed Tamimi” and with “Fake News” stamped across it in red was based on Mohammed's version of events, which he repeated several times. “The truth is always our guiding light and we will continue to present the truth in order to expose the Palestinian incitement apparatus,” it said.

“A surgeon removed the bullet from Tamimi's skull after he allegedly fell off his bike,” said Amit Gilutz, from the Israeli human rights organization B'Tselem. He said that the arrest of a 15-year-old as he awaited surgery to replace part of his skull after being shot in the head is “testament to just how little regard Israeli authorities have for the well-being and lives of all Palestinians, including minors.”

“Having been interrogated under such conditions, it's no wonder if Tamimi indeed confessed to sustaining the injury due to a bike accident,” he said. “He may as well have confessed to it being the result of a dolphin-back-riding accident in the sea of Nabi Saleh.”

Sufian Taha and Ruth Eglash in Jerusalem contributed to this article.