Shunsuke Mutai, the vice-minister of reconstruction, was visiting the town of Iwaizumi to assess the deadly damage caused by Typhoon Lionrock.
The storm killed more than 20 people in the region.
But he was seen on TV laughingly being piggybacked by a less senior official, so he could keep his feet dry.
Mr Mutai, who apparently forgot to take rubber boots with him, later apologised, saying what he did was "inappropriate" and that he "deeply regretted it".
The picture went viral on social media with netizens lambasting the vice-minister and accusing him of not taking his job seriously.
Chief Cabinet Secretary Yoshihide Suga later criticised Mr Mutai for lacking sensitivity.
"He went there as head of the government investigation team, so naturally he should have brought his rubber boots to begin with.
"I must say he lacked sensitivity to the residents and the region," he said.

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Philippe Coutinho scored the only goal in the quarter-final replay to book a last-four tie with Aston Villa.
It came after defeats by Manchester United and Arsenal brought criticism and reports of "crisis talks".
"A lot has been made of that meeting but the review was very important in how we want to work," said Rodgers.
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"I'm a coach who speaks openly to players. If you don't review and analyse your performance, how can you get better?"
Rodgers said this week's meeting had been no different to the others he held during the impressive 12-match run that yielded 32 points before those recent defeats.
"It's something that we've done all year," said Rodgers.
"It provides us the lever to move forward - how can we be better, how can we improve?
"I'd seen all of this about saving our season. It wasn't about saving our season.
"We just needed to stay calm. Our two performances against Arsenal and Manchester United weren't to the standards we'd set for three months."
Liverpool will now face Aston Villa in the semi-final at Wembley on Sunday, 19 April.
Henderson's perfect present
The victory was particularly significant for captain for the day Jordan Henderson as it came hours after the birth of his second daughter.
"His wife had a child during the night. Jordan had to go away, he hadn't slept much and then travelled all the way back again.
"He said 'boss, as soon as the baby's out, I'll be coming back'."
Mixed emotions for Ince over Gerrard send-off
Paul Ince is hoping his old club Liverpool will win the FA Cup in former team-mate Steven Gerrard's final match for the club on his birthday, 30 May. There will still be a sense of regret though.
"It would be nice for Steven Gerrard to finish at Liverpool by winning something," Ince said on BBC Match of the Day.
"But I wish it had been the Premier League. Someone of his greatness should have won the Premier League."
A Japanese senior government official has come under criticism for hitching a ride on a colleague's back to cross a puddle.
[NEXT_CONCEPT]
A Liverpool team meeting after recent defeats had a key role in their FA Cup win at Blackburn, according to manager Brendan Rodgers.