Authorities are searching for a fourth suspect, the officials added, speaking on condition of anonymity because they were not authorized to talk to the media.
The Israeli government could not be reached for comment on Shabbat.
The arrests were based on information extracted from a retired Lebanese general arrested earlier this week, also for allegedly spying for Israel.
The general, his wife and his nephew, who is a government security agent, were charged this week with espionage.
According to charges filed Thursday by the military prosecutor Saqr Saqr, the three provided information to Israel about Lebanese and Syrian military and civilian installations.
Lebanon considers itself at war with Israel and bans its citizens from having any contact with the Jewish state.
Lebanese authorities have made a series of arrests in recent months that appear to be part of a stepped-up campaign against those suspected of gathering information on Hezbollah militants for Israel. The Iranian-backed Hezbollah guerrilla group fought a 34-day war with Israel in 2006 that killed 1,200 people in Lebanon and 159 in Israel.
The retired general had worked for the General Security Department at the Interior Ministry, the same office that employed his nephew. He told interrogators he had worked for Israel for more than 10 years and regularly met with his Israeli contacts at European destinations.