Netanyahu has been charged with bribery and fraud and breach of trust in three corruption cases, CNN reported.
Attorney General Avichai Mandelblit submitted the indictment in the Jerusalem District Court shortly after Netanyahu withdrew his request for parliamentary immunity, a request he was almost certain to lose.
Netanyahu has insisted he is innocent, calling the investigations an "attempted coup" driven by the left and the media.
The charges in court mean that Netanyahu will be the first sitting prime minister to face trial in the country's history. A trial date has not been set yet, but the legal process could possibly take years.
Under Israeli law, Netanyahu does not have to resign upon indictment. Instead, he only has to resign if he is convicted and that conviction is upheld through the appeals process.
The Knesset was due to start debating on Tuesday whether to convene the committee tasked with weighing the immunity request.
Lawmakers appeared certain to reject his bid, a factor likely to have influenced Netanyahu's decision not to proceed.
The Trump administration's plan to end the Israeli-Palestinian conflict will be released with Netanyahu standing next to Trump, in a powerful image for Israel's embattled leader, reinforcing his claim that this is a "historic" opportunity.
"At this fateful hour for the people of Israel, while I am in the United States on a historic mission to shape the final borders of Israel and safeguard our security for generations to come, another show in the immunity-removal circus is set to begin," Netanyahu wrote on his Facebook page before his indictment.
"This is the continuation of a personal and obsessive hunt against me by the 'Anyone But Bibi' people. Instead of understanding the magnitude of the hour and rising above political considerations, they continue to deal in cheap politics that endangers a crucial moment in the history of the nation.
"I will not allow my political opponents to use this matter to interfere with the historical move I'm leading," he said.
Rival Benny Gantz, whose Blue and White party emerged the largest in the Knesset after the last elections, said Netanyahu cannot lead the country and also deal with his legal problems.
"Netanyahu goes to trial. We must proceed," Gantz said on Twitter.
"The citizens of Israel have a clear choice a Prime Minister that will work for them or a Prime Minister dealing with himself. No one can run a country and at the same time run three severe criminal cases on bribery, fraud and breach of trust."
( With inputs from IANS )