Israel's military said troops killed a Palestinian militant leader and six others on Thursday, the second day of large-scale "counter-terrorism" operations in the occupied West Bank.

A military spokesman gave an overall death toll of 16 Palestinian militants since Israeli forces launched coordinated raids across the northern West Bank on Wednesday. The Palestinian health ministry reported at least 15 dead.

A military statement said five were killed on Thursday in the Tulkarem refugee camp including Muhammad Jaber, also known as Abu Shujaa. Palestinian militant group Islamic Jihad said he was its commander in the nearby Nur Shams refugee camp.

According to Israeli military spokesman Lieutenant Colonel Nadav Shoshani, "he was a head of a terror network in Nur Shams," also accusing Jaber of "inciting" young Palestinians to carry out attacks against Israelis.

Shoshani told an online media briefing that Jaber was killed in "a significant exchange of fire" between Israeli forces and "armed terrorists hiding" in a mosque in the Tulkarem camp.

Tulkarem governor Mustafa Taqatqa rejected the army's account, saying the five men were not inside the mosque when killed.

"A rocket was fired at a house and the young men were not in the mosque," said Taqatqa.

Shoshani said that one member of the Israeli security forces was injured in the operation that killed Jaber.

The military separately said it killed two "terrorists" in Jenin, also in the northern West Bank, taking its reported death toll of Palestinian militants to 16 since the raids began early on Wednesday.

According to the military, nine of them were killed on Wednesday, the first day of the simultaneous raids. (AFP)