The indictment, announced by Attorney General Avichai Mandelblit, poses no immediate threat to Netanyahu's decade-long hold on power, a grip loosened by elections in April and September in which neither the far-right Likud leader nor right-wing challenger Benny Gantz secured a governing majority.
Under Israel's law, Netanyahu does not have to resign despite being charged. The opening of a trial could be delayed for months by a possible new election and any moves by Netanyahu to secure parliamentary immunity from prosecution.
"This is a difficult and sad day," Mandelblit said, announcing the indictment in a televised statement. Mandelblit, who was appointed to his post by Netanyahu, said he had a duty to Israel's citizens to ensure that no one was above the law.
Police recommended in February that Mandelblit file criminal charges against Netanyahu in the long-running investigations dubbed Cases 1000, 2000 and 4000.
Netanyahu is suspected of wrongfully accepting US$264,000 worth of gifts from tycoons and of allegedly dispensing favors in return for favorable stories about him in Israel's biggest-selling newspaper, Yedioth Ahronoth, and the Walla website.
Case 4000, the most serious of the three, alleges that Netanyahu granted regulatory favors worth about 1.8 billion shekels (about US$500 million) to Israel's leading telecommunications company, Bezeq Telecom Israel.
In return, Mandelblit said, Netanyahu and his wife often received positive coverage on the Walla site, which is owned by Bezeq's former chairman, Shaul Elovitch.
He indicted Netanyahu on charges of breach of trust and fraud in all three corruption cases against him, as well as bribery in Case 4000.
Netanyahu, in power since 2009, has denied wrongdoing in three corruption cases, claiming he is the victim of a political witch hunt.
Commenting on the announcement, Palestine Liberation Organization official Wasel Abu Youssef said that for years Netanyahu had sought to avoid this outcome by "launching wars against the Palestinian people" to boost his domestic popularity.