Projects financed by the $150 billion fund include roads in Okinawa, an ad campaign for Japan’s tallest building and support for whaling research.
Some 325,000 people remain displaced 18 months on from the disaster.
In some areas little reconstruction work has been carried out, reports say.
Some 19,000 people were killed or remain missing following the tsunami and earthquake that struck north-east Japan in March 2011.
The government has passed a number of supplementary budgets to fund reconstruction efforts in affected areas.
But a government audit showed money had been used for unrelated projects reportedly included on the basis that they could boost national economic revival.
The findings come at a time when questions are being asked about the speed of Japan’s reconstruction effort.
Takashi Kubota, deputy mayor of Rikuzentakata, a fishing port where nearly half of the houses were destroyed, told the Associated Press news agency that “not one single new building yet” had been built in the destroyed downtown area.
“In 19 months, there have basically been no major changes,” he said.
Speaking in parliament on Monday, Japanese Prime Minister Yoshihiko Noda promised that problems would be addressed.
“There have been various criticisms made regarding how the budget for reconstruction has been spent,” he said.
“We must listen sincerely to the voices calling for the utmost priority to be accorded to disaster area reconstruction. We will properly provide allowances for budget items that are truly needed by the disaster-affected areas and strictly narrow down other items.”
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