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.
"Trips by Mr. Netanyahu and his family, funded by external bodies during the period in which he served as finance minister, deviated from regulations on the subject and as such could give the appearance of obtaining a benefit or of a conflict of interest," the Hebrew-language document published on the comptroller's official website said.
It said that the premier did not report the funding to the necessary state oversight bodies.
"Mr. Netanyahu did not apply to the gifts committee or the permits committee in order to ascertain if in receiving outside funding there was acceptance of a benefit or a prohibited gift," it said.
State Comptroller Yosef Shapira, tasked with overseeing the use of public funds, investigated allegations of double billing of flights, initially reported by the Haaretz and Yediot Aharonot daily newspapers -- both hostile to Netanyahu.
He also looked into an allegation that bonus points from Israeli carrier El Al earned through official travel were used by Netanyahu's relatives for private trips.
The report did not allege criminality by Netanyahu but said some of its findings had been passed to the attorney general's office and could therefore not be publicised while the subject of its checks.
Signup to our newsletter and follow us on Facebook and Twitter!
"In light of the attorney general's examination into these and other matters there are issues related to the subject which the state comptroller cannot examine in the context of this report," it said.
Media reports also said Shapira is concerned that former attorney general Yehuda Weinstein stalled on investigating, before the case was dropped.
Incumbent Avichai Mandelblit said in televised remarks that such concerns were unfounded and pledged that he would deal with the issue "without delay."
"The examination must be carried out honestly and objectively," he said.
Privately owned Channel 2 television reported that the police have renewed an inquiry into the allegations to determine whether to open a formal investigation.
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.
In February, however, he began a 19-month sentence for bribery and obstruction of justice.