Governor Nyesom Wike looked on as the Prodest Home and Etemeteh were demolished on Sunday.
Both hotel managers have been arrested, but the brother of the manager of Prodest Home has told the BBC that the hotel was following the lockdown rules.
Despite criticism on social media, Governor Wike defended the decision, saying they had found positive cases in hotels across the state.
"Look at the rate of infections, most of these people are found in hotels," he said.
He, however, did not say if the two demolished hotels were hosting people with coronavirus.
Nigeria’s Centre for Disease Control has confirmed 21 cases and two deaths in Rivers state.
Meanwhile, in Lagos, Governor Babajide Sanwo-Olu has warned that lockdown measures could be reintroduced if residents of the country's largest state ignored social distancing rules.
Nigeria has recorded 4,399 cases of Covid-19 and reported 143 deaths.