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.
A Japanese senior government official has come under criticism for hitching a ride on a colleague's back to cross a puddle.