Segev, a former doctor whose medical license was revoked, was released from prison in 2007 and had been living in Africa in recent years.
The Shin Bet said Segev met his operators twice in Iran, and also met Iranian agents in hotels and apartments around the world. Segev was given a "secret communications system to encrypt messages" with his operators.
The statement said that Segev maintained connections with Israeli civilians who had ties to the country's security and foreign relations. It said he acted to connect them with Iranian agents who posed as businessmen.
Israel and Iran are bitter enemies, and the allegations against Segev are extremely grave. Israel considers Iran to be its biggest threat, citing Iranian calls for Israel's destruction, Iran's support for hostile militant groups like Hizbollah and its development of long-range missiles.
Prime Minister Benjamin Netanyahu has been an outspoken critic of the international nuclear deal with Iran and welcomed the US decision to withdraw from the deal. More recently, Israeli forces have carried out a number of airstrikes on Iranian forces in neighbouring Syria.
It is unclear what motivated Segev, whether it was out of monetary or idealistic reasons. It is also not immediately known how much damage, if any, he caused Israel.
An indictment was filed against Segev last week. A gag order was imposed on the case and there were no further details.
-AP