The 450-page report by a 10-member panel of independent experts was released on Monday, and comes as anti-nuclear activists continue a vociferous campaign against the restarting of two nuclear reactors in the country.
The government is currently readying a new energy policy, due next month.
The panel suggested that post-Fukushima safety steps taken at nuclear power plants across the country have not been enough to cope with a complex catastrophe, a combination of human error and natural causes, such as the one that struck the country after an earthquake and tsunami last year.
"We understand that immediate safety measures are being further detailed and will materialise in the future. But we strongly urge the people concerned to make continued efforts to take really effective steps," said the panel, chaired by University of Tokyo engineering professor Yotaro Hatamura.
Tokyo Electric Power Co (Tepco), the operator of the Fukushima Daiichi plant, and regulators failed to plan for a massive natural disaster, the panel said, blaming them for being lulled by the same "safety myth" blasted by a parliament-appointed team of experts earlier this month.
"Both the government and companies should establish a new philosophy of disaster prevention that requires safety and disaster measures against any massive accident and disaster... regardless of event probability," the report said.
The inquiry did not go as far as accusing regulators and TEPCO of "collusion", as a parliamentary panel had done earlier this month.
The decision to restart two reactors operated by the Kansa Electric Power Company has energised Japans' anti-nuclear movement, with more than 100,000 people taking to the streets in Tokyo a week ago.
All 50 of Japan's nuclear reactors were shut down for safety checks after the Fukushima disaster. Critics say that the two restarted reactors do not meet the government's new safety criteria, announced this April.
The panel has called on the government to take immediate action on certain issues, such as ensuring off-site nuclear accident management centres are protected against the kind of massive radiation leaks that rendered the one at Fukushima unusable.
The Fukushima Daiichi plant, located 240km north of Tokyo, was hit on March 11 last year by an earthquake and tsunami that knocked out power and cooling systems.
Three of its six reactors went into meltdown, and about 150,000 people were forced to flee the area as radioactive material leaked into the surroundings.
The panel said that there was no proof that the earthquake was a key factor in the disaster, but added that a certain degree of impact could not be ruled out.
TEPCO's own investigation put the blame for the accident solely on the tsunami.
The panel, however, called on TEPCO to review data that had been presented to it, saying that it believed that it contained errors. It said that further investigations should be carried out.
The report also blamed the country's nuclear regulators for not paying sufficient attention to improvements in nuclear safety standards, as recommended by the International Atomic Energy Agency (IAEA).
It said that the Japanese Nuclear Industrial and Safety Agency had been promoting nuclear energy without being open about the inherent risks.
It said that a culture of complacency about nuclear safety and poor crisis management had led to the nuclear disaster.
The panel's investigation concludes the last of a series of probes into the worst atomic accident since the Chernobyl disaster in 1986.