The International Olympic Committee had been seriously considering moving the vote on whether to choose Los Angeles or Paris to a new venue because of the troubles.
IOC president Thomas Bach said: "On this occasion the Peruvian government has given us all necessary assurances that the IOC session will be organised in a great way."
A statement added: "Following the devastating floods affecting large parts of the country, the International Olympic Committee and the Peruvian government today confirmed that preparations for the IOC Session, to be held in Peru, in September are going ahead as planned."
"The eyes of the world will be on Lima and we believe that hosting the IOC session will send a vital message to the world and to Peru that we are ready to welcome the world after the emergency situation.
"In addition, the event will bring positive international attention to the country as we receive several heads of state, many high-level government officials and over 2,000 international press members.
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