Japan's disaster reconstruction minister Masahiro Imamura resigned Wednesday, a day after saying it was "a good thing" the March 2011 earthquake and tsunami struck northeastern Japan rather than the Tokyo area.

Prime Minister Shinzo Abe picked Masayoshi Yoshino, a House of Representatives member from Fukushima Prefecture and a former senior vice environment minister, to replace Imamura.

Imamura tendered his resignation to Prime Minister Shinzo Abe on Wednesday morning and the prime minister accepted it immediately.

"I severely troubled and hurt people in (northeastern Japan)," Imamura told reporters at the prime minister's office after submitting his resignation.

 "I apologize from my heart for my lack of virtue," he added, while rejecting calls to also resign as a lawmaker.

Abe also apologized, both to the residents of areas recovering from disasters and to the Japanese public at large, after accepting Imamura's resignation.

Imamura made the "good thing" comment at a function in Tokyo for a faction of the ruling Liberal Democratic Party, which Abe was also attending, on Tuesday evening. He immediately retracted the remark and apologized, but the damage was done.

Imamura had prompted calls for his resignation earlier this month when he suggested people displaced by the Fukushima nuclear disaster triggered by the quake should fend for themselves.

The leader of the main opposition Democratic Party on Wednesday said Imamura's resignation is not enough on its own.

"This brings into question Prime Minister Shinzo Abe's responsibility for having appointed (Imamura)," Renho said at a party meeting.

Abe acknowledged that this responsibility lies with him in his apology. "(The administration) must take seriously the suggestions that we are becoming slack," Abe said, vowing to "bring back the public's trust."

Imamura, a native of Saga Prefecture in Japan's southwest, was given his post in a Cabinet reshuffle in August last year.

His replacement Yoshino hails from Iwaki, a city in Fukushima on the Pacific coast that bore the brunt of damage in the 2011 disaster at the Fukushima Daiichi nuclear complex.

"I have been making reconstruction my life, so I'm happy to be given a challenging post," Yoshino told reporters at the LDP's head office in Tokyo on Wednesday morning.

Imamura's resignation has prompted the suspension of House of Representatives proceedings scheduled for Wednesday morning and most of the House of Councillors proceedings scheduled for Wednesday.