The dithering is preventing the government, whose debt is already twice the size of the country's GDP, from getting the most bang for every buck.
"You've got economic malaise and political as well. That's just a recipe for disaster," said Matthew Circosta, an economist with Moody's Analytics in Sydney.
Part of the problem is the central government's strategy of managing the reconstruction from Tokyo instead of delegating it to provincial governments. At the same time, the local governments lack the staff and expertise for such major rebuilding.
The government "thinks it has to be in the driver's seat," Jun Iio, a government adviser and professor at Tokyo University told a conference in Sendai. "Unfortunately the reconstruction process is long and only if the local residents can agree on a plan will they move ahead on reconstruction."
"It is in this stage that creativity is needed for rebuilding," he said.
Even Sendai, a regional capital of over 1 million people much better equipped than most coastal communities to deal with the disaster, still has mountains of rubble. Much of it is piled amid the bare foundations, barren fields and broken buildings of its oceanside suburb of Arahama.
Sendai quickly restored disrupted power, gas and water supplies and its tsunami-swamped airport. The area's crumbled expressways and heavily damaged railway lines were repaired within weeks.
But farther north and south, ravaged coastal towns remain largely unoccupied.
More than 240 ports remain unbuilt; in many cases their harbors are treacherous with tsunami debris.
Like many working on the disaster, Yoshiaki Kawata of Kansai University worries that the slow progress on reconstruction will leave the region, traditionally one of Japan's poorest, without a viable economy.
"There is almost no one on the streets," he said in the tiny fishing hamlet of Ryoishi, where the sea rose 17 meters (56 feet). "Building a new town will take many years."