Projects ranging from counting sea turtles on semi-tropical beaches, to the promotion of cheese and wine events hundreds of kilometres (miles) from the disaster zone benefitted from the largesse, a report said.
The admissions are the latest in a series of apparent embarrassments for the Japanese government, which has previously acknowledged the country's controversial whaling programme was being supported by disaster money.
The Asahi Shimbun, a major daily newspaper, surveyed local authorities around the country to find out what happened to the 200 billion yen Tokyo set aside for economic reconstruction after the disaster.
In a town in southern Kagoshima prefecture, which lies around 1,300 kilometres (800 miles) from the devastated city of Ishinomaki, three million yen was spent on the protection and observation of sea turtles.
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Ten people were employed to count the creatures as they came ashore and to remind sightseers not to interfere with them.
"We only counted sea turtles and were not required to move eggs to safe places or do other things. It wasn't even for sea turtles, let alone those hit by the disaster," the daily quoted one of the 10 as saying.
"Those who were hit by the disaster were widely spread across the nation at that time and supply chains (for manufacturing industries) were disrupted," said an official at the ministry.
More than 18,000 people died when the towering tsunami smashed into Japan's northeast in March 2011.
Vast stretches of coastline were devastated and hundreds of thousands of people were made homeless in the catastrophe, which also set off a nuclear crisis at Fukushima.