The boarding school has been shut and the army, which is leading rescue operations, is moving in to take the almost 200 students to safety.
About 1.5 million people in total have been affected by Cyclone Idai's torrential rains and winds that have reached speeds of up to 200 kilometers, or 124 miles, per hour, according to the United Nations.
The cyclone weakened as it moved into eastern Zimbabwe, Ish Mafundikwa reports for NPR.
Heavy rains are forecast to continue into the middle of the week, bringing more flooding and making it hard to reach stranded communities in both Mozambique and Zimbabwe.
Local officials said a helicopter provided by the military was failing to access marooned villagers due to mist and strong winds, severely limiting the rescue effort.
"The immediate needs for people is shelter. because most people have been displaced", he said.
Jacob Mafume, a spokesman of the opposition Movement for Democratic Change (MDC) warned in a tweet that a "serious humanitarian crisis" is unfolding in the region. Their statement of March 18 said in part: "While the physical impact of Idai is beginning to emerge, the human impact is unclear".
President Emmerson Mnangagwa's government has declared a state of disaster in the affected areas and has had to hurry back from an official trip to the United Arab Emirates.
President Filipe Nyusi, who cut short a working visit to eSwatini, was expected to fly to Beira. Many families now lack basic supplies like food and water, with the situation likely to get even worse as flood waters rise.
Beira global airport was briefly shut after the air traffic control tower and navigation equipment were partially destroyed by the cyclone.
Mozambique and Malawi, two of the poorest countries in the world, are prone to deadly flooding during the rainy season and chronic drought during the dry season.
The rain also affected neighboring Malawi, where 56 people died, the government said.
Eskom, South Africa's power utility, said the storm reduced the amount of electricity it imports from the Cahora Bassa hydropower dam in Mozambique, exacerbating a shortage that's resulted in blackouts.