The research comes as a Tokyo cinema holds a week-long festival of films on the death penalty, and amid continued pressure from rights groups who say Japan should join most other advanced economies in abolishing the practice.
Mai Sato, a criminology researcher at Britain's Oxford University who led the study, said when the public is asked to make an informed choice on the death penalty, many more people are opposed.
The last government poll on the subject, in 2009, showed 86 per cent of those questioned supported the death penalty, a figure Tokyo frequently cites to defend the practice.
Rights groups say it is barbaric, partly because inmates can languish in solitary confinement on death row for years or even decades, and are only told of their impending hanging a few hours in advance.
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Some of Japan's death row prisoners have been there for decades. They include Iwao Hakamada, now in his late 70s, who was convicted of the 1966 murder of his boss and the man's family.
In a multi-stage survey of 20,000 Japanese people, Sato sorted respondents into equal groups of those for, against and undecided on the subject.
She then divided them into two sets where one was given a detailed explanation of the execution process and the potential for miscarriages of justice, while the other was not.
Results showed that in the first group, 36 per cent supported retaining capital punishment compared to 46 per cent in the second.
Sato said the results showed that government polls were too simple and needed to be refined.
Though no executions took place in 2011, eight inmates have been hanged since Abe came to power in December 2012.
The Japan Federation of Bar Associations, which has long opposed capital punishment, criticised the government poll last November.
In response to an AFP question, the government acknowledged there had been criticism of its methodology, but declined to comment on its future course of action.
The findings came as a Tokyo cinema runs a series of eight films from around the world intended to provoke debate, as well as an exhibition of paintings by some of Japan's 129 death row inmates.
"In Japan, information about the death penalty is not publicly and widely available," she said. "Despite that, executions are taking place.