Akira Amari unexpectedly made the announcement at a press conference in Tokyo on January 28.
He again denied personally receiving bribes from a construction company, as had been alleged by a Japanese magazine.
The development will be seen as a significant blow for PM Shinzo Abe.
Akira Amari, who has been minister of state for economic and fiscal policy since late 2012, has been widely described as one of Shinzo Abe’s most trusted members of parliament.
As Japan’s lead negotiator for the Trans Pacific Partnership (TPP) agreement, Akira Amari was expected to travel to New Zealand next week to sign the agreement.
He was also regarded as the architect of Abenomics – Shinzo Abe’s plan to pull the world’s third largest economy out of deflation.
Akira Amari will be replaced by Nobuteru Ishihara, formerly the country’s environment minister.
A local magazine had reported last week that Akira Amari and his aides were given money and gifts worth some 12 million yen ($101,000) by a construction company in return for some favors linked to land ownership.
Akira Amari said he did receive money which he wanted declared as a political donation, however, he said some of it was mishandled by his staff.
Japan’s economy, which has been struggling with deflation for nearly two decades, avoided a technical recession in Q3 of 2015.
“Japan is finally emerging from deflation,” Akira Amari told the press conference, as reported by Reuters.
“We need to pass legislation through parliament for steps to beat deflation and create a strong economy as soon as possible.
“Anything that hampers this must be eliminated, and I’m no exception,” Reuters reported him as saying.
“I, therefore, would like to resign as minister to take responsibility [for what my aide has done],” he said, according to Reuters.
Akira Amari is the fourth member of Shinzo Abe’s cabinet to resign amid allegations of bribery, among other issues.
Pm Shinzo Abe has apologized for the latest resignation.
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