The spokesman said that the suspected leader, Al'a Abu al-Rob, was killed when he opened fire at Israeli forces that had broken into his home. Israel said weapons and explosives were discovered in al-Rob's home during a search.
However, al-Rob's brother said that Israeli troops barged into their home and shot his brother dead while he sat at a computer.
Al-Rob headed Islamic Jihad in the village of Qabatiya just to the south of Jenin. He has been on Israeli's wanted list for over 18 months in connection with attacks on Israel.
Military search operations are carried out in the West Bank almost daily and dozens of Palestinians have been arrested by Israel on suspicion of terrorist activities.
However, Palestinian sources in Jenin told the Israeli Ynet news agency that Israeli troops had not killed al-Rob, who is being held by Palestinian security services, but another man with a similar name