The state comptroller's report covers 2003-05, when Netanyahu was finance minister, and concerns five foreign trips, some with his wife and children, Israeli media reported.
State Comptroller Yosef Shapira, who is tasked with overseeing the use of public funds, was investigating allegations of double billing of flights, reported the Haaretz and Yedioth Ahronoth daily newspapers -- both hostile to Netanyahu.
The report, expected to be released later today, is said to note a "lack of clarity" over bonus points earned on flights by the Israeli company El Al during official trips, they reported.
Privately owned Channel 2 television reported the police have renewed an inquiry into the allegations to determine whether to open a formal investigation.
The reports also alleged Shapira is concerned former attorney general Yehuda Weinstein stalled on investigating, before the case was eventually closed.
Netanyahu's lawyer dismissed the allegations, saying they had previously been looked into and nothing improper had been found.
"There is nothing in the report of the state comptroller," Yossi Cohen, the lawyer for the Netanyahu family, told public radio.
Former prime minister Ehud Olmert also faced allegations of double billing in a travel case, though it was later dropped.
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