Metzger, who stepped down from the role after 10 years on July 24, had been arrested and questioned on similar charges in June. He was eventually released without charges being pressed.
A police statement today said the national fraud unit put the sums related to the suspected felonies at millions of shekels.
Metzger's first questioning at the national fraud unit headquarters in Lod, south of Tel Aviv, came after months of covert investigations.
Israel has two chief rabbis, the Ashkenazi and Sephardi, whose responsibilities include the country's rabbinic courts and regulating the food supervision industry.
Also Read
Metzger was voted into the prestigious position in 2003 due to the support of the senior ultra-Orthodox rabbinic authority at the time.
In 2005 he was questioned on suspicion of receiving benefits from a hotel in Jerusalem in return for favours, and police recommended he be tried for fraud and breach of trust.
Instead he wrote a scathing report about the rabbi, accusing Metzger of lying to police and recommending that he resign immediately.