Details of the agreement between Ari Harow and the prosecution have been placed under a gag order by a court, with an Israeli official only confirming to AFP that a deal has indeed been sealed.
Harow, a US-born Israeli immigrant, worked for Netanyahu from 2009-10 and 2014-15, when he stepped down over allegations of corruption.
He has been under investigation for more than two years on suspicion of bribery, breach of trust, conflict of interest and fraud, media reports said.
According to reports, Harow has already been supplying investigators with information regarding two of the ongoing investigations into Netanyahu.
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One is based on suspicions that the premier unlawfully received gifts from wealthy supporters, including Australian billionaire James Packer and Hollywood producer Arnon Milchan.
Also being probed is a suspicion that Netanyahu sought a secret deal with the publisher of top-selling daily Yediot Aharonot.
The proposed deal, which is not believed to have been finalised, would have seen Netanyahu receive positive coverage in return for him helping scale down the operations of Israel Hayom, Yediot's main competitor.
Meanwhile, authorities were investigating another affair involving alleged corruption around a deal to buy submarines from Germany's ThyssenKrupp.
Netanyahu himself is not a suspect in the case, but his second cousin and family lawyer David Shimron represented ThyssenKrupp and was arrested for questioning last month before being released.
The investigations have stirred Israeli politics and led to speculation over whether Netanyahu will eventually be forced to step down, which he is not formally obliged to do even if testimony is given against him.
Netanyahu has rejected any allegations of misconduct in all the affairs, saying repeatedly that he is the target of a campaign by political opponents.
In 2000, prosecutors decided there was insufficient evidence to indict Netanyahu and his wife Sara following an investigation.
The probe then looked at whether they unlawfully kept gifts presented to Netanyahu during his first term as premier between 1996 and 1999.
It also investigated whether the Netanyahus had promised a Jerusalem contractor that he would be paid out of the public purse for work done on their private residence.
In a short video posted on his Facebook page on Friday, Netanyahu discussed a number of issues from the last week, offering a fleeting reference to the latest legal developments and saying he would not comment on "background noises".