Sara Netanyahu was charged on Thursday along with Ezra Saidoff, a former deputy director general of the Prime Minister's Office.
Netanyahu was the subject of a long police probe into allegations that she had falsified household expenses, including claims she had spent "over 350,000 shekels" ($96,500, €83,500) on catering for the premier's office.
Sara Netanyahu's indictment comes as Israeli Attorney General Avichai Mandelblit weighs indicting her husband in several open investigations over fraud and breach of trust allegations that threaten his career.
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"Sara Netanyahu is a strong and honourable woman and there has never been any fault in her actions", a statement on the prime minister's Facebook page said.
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From 2010 to 2013 Netanyahu, her family and guests received "fraudulently from the state hundreds of prepared meals (each including a number of courses) to the value of 359 000 shekels (R1.3 million)", the indictment read.
She is alleged to have falsely stated there were no cooks available at the prime minister's official residence. If convicted, she could face a maximum sentence of five years behind bars for the most serious charge, though that appeared unlikely.
"They're dealing with the most important things in the world", he said at the time.
The indictment, slated to be presented in May, was delayed after it emerged that Nir Hefetz, a former close adviser to the Netanyahu family, had provided new evidence against Netanyahu. The Israeli prime minister is himself embroiled in a series of corruption investigations but has protested his innocence and vowed to remain in power, saying he is the victim of a witch-hunt.
Police are still investigating suspicions Netanyahu arranged regulatory benefits for the country's biggest telecommunications provider, Bezeq Israeli Telecommunication Corp., in exchange for sympathetic coverage by its online news outlet.