The waters of the Chari river had risen by more than eight metres (26 feet) in the last 10 days or so, Prime Minister Allamaye Halina said.
N'Djamena, Chad's capital, is located where the Logone and Chari rivers flow into each other, and both rivers had been swollen by the heavy rains, Halina said.
The severe flooding in Chad since July has already affected around 1.7 million people, destroying 164,000 homes and flooding 250,000 hectares of farmland, and drowning 60,000 heads of cattle.
The floods have spared none of the country's provinces.
Already in early September, the UN warned of the impact of "torrential rains and severe flooding" in the wider region, particularly in Chad.
It called for immediate action and funding to tackle climate change.
The heavy rains across the region have killed more than 1,500 people in Chad, Niger, Nigeria, Cameroon, Mali and Burkina Faso and Guinea, according to the International Organization for Migration (IOM).
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