News of the arrest was released just hours after Prime Minister Benjamin Netanyahu left for Washington and New York, determined to expose what he described as "sweet talk" by Israel's arch-foe Iran.
The suspect, holding a Belgian passport, was sent to Israel by Iran's elite Republican Guards and arrested at Tel Aviv's Ben Gurion international airport, Shin Bet charged in a statement.
The domestic intelligence service identified him as Ali Mansouri, 58, and said he had enrolled in a "special operations unit of the Revolutionary Guards responsible for numerous terrorist attacks around the world."
The Shin Bet said that under questioning, the suspect had said he had been promised USD 1 million to use his position as a businessman to set up companies in Israel on behalf of the Iranian intelligence services to "harm Israeli and Western interests."
More From This Section
He had previously visited Israel in July 2012 and last January. An Iranian national, the suspect had in 2006 married a Belgian woman whom he had since divorced.
On the diplomatic front, Netanyahu has been dismissive in his response to the drive by Iran's new President Hassan Rouhani to mend fences with the international community, which culminated in a historic 15-minute telephone conversation with US President Barack Obama on Friday.
Israeli leaders have repeatedly vowed to take military action rather than see Iran develop a bomb and have called on its US ally to take tougher action against Tehran, saying they see no real change of policy under Rouhani.