Its agents and police had arrested Anas Haj Yahya, 35, from the northern town of Taibe, on January 29 "in the wake of intelligence information which pointed to him as someone working to promote terror within the state of Israel".
He was formally charged on Monday in a court in Lod, central Israel, Shin Bet said in a statement, without detailing the charges.
"During interrogation by the Shin Bet, it became clear that he was in contact with 'Islamic State' activists" through internet forums, the Hebrew-language statement said.
"Among items seized at his home were pictures of military material and explosive charges," the statement added.
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Several Arabs from northern Israel have been arrested for alleged links with IS and around 50 Arab Israelis are currently believed to be among its ranks in Syria and Iraq.
Israel added IS to its list of terrorist organisations in October 2015.
Arab Israelis are the descendants of Palestinians who remained on their land after the creation of the state of Israel in 1948.