Alice Kayitesi said the Wednesday morning incident happened in the Nyabarongo river.
“He had broken the stay-home rule, he’s among very few people here who are not co-operating with the lockdown to stop the [corona]virus,” Ms Kayitesi said.
The East African nation has confirmed 40 cases so far, the highest in the region.
The shutdown of economic activities in the country has severely affected majority of people who are low-income earners.
The government said that it would help those struggling amidst the strict measures.
In an another development, a local news website reported on Monday that police shot dead two men in the southern district of Nyanza after an altercation about the lockdown.
The police have, however, not confirmed the incident.