Metzger's questioning at the national fraud unit headquarters in Lod, south of Tel Aviv, comes after months of covert investigations involving three other suspects, according to police.
On Thursday, police "searched the homes and offices of the suspects, including those of Rabbi Metzger," the statement said. "Documents, computers and other materials were seized."
Officers questioned Metzger on suspicion of "receiving bribes, theft, breach of trust and money laundering," the statement read.
It added that the three other suspects would appear before a magistrates' court near Tel Aviv later Thursday.
Israel has two chief rabbis, the Ashkenazi and Sephardi, whose responsibilities include the country's rabbinic courts and regulating the food supervision industry.
Metzger was voted into the prestigious position in 2003 thanks 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 al-Quds (Jerusalem) in return for favors, and police recommended that he be tried for fraud and breach of trust.
But then-attorney general Menachem Mazuz, fearing an unsuccessful prosecution, in 2006 decided against serving an indictment.
Instead he wrote a scathing report about the rabbi, accusing Metzger of lying to police and recommending that he resign immediately.
Metzger's term is due to end shortly, with elections for new chief rabbis due no later than July 24.