Rice plants generally die if they remain submerged for about four days.
"The cyclone certainly complicates matters," said Paul Risley, a spokesman with the UN's World Food Programme in Bangkok.
"It blew through the critical rice-growing areas of the country and it seems the harvest was only partially completed. This could represent a substantial loss to the country's rice output," he said.
According estimated by the Rome-based UN Food and Agriculture Organization the five states hit hardest by the cyclone on Saturday produce 65 per cent of the country's rice.
The region also is home to 80 per cent of its aquaculture, 50 per cent of its poultry and 40 per cent of its pig production, the FAO said.
With as many as a million people directly affected by the catastrophe, rice shortages and possible accompanying public resentment present a major challenge to the country's military government.
With food shortages and rising prices already triggering riots in poor countries, the cyclone's disruption of the harvest in one of Asia's richest rice-growing areas could also have global implications.
Until last weekend, Myanmar had been expected to export a portion of its rice harvest.
Shortfalls could hit Sri Lanka, Bangladesh and other regional neighbours that had been counting on importing Myanmar's rice.
Traders suggest that in the cyclone's wake, world rice prices, already soaring, could be sent higher.
Globally the cost of rice has already nearly tripled since the beginning of the year, busting the budgets of humanitarian agencies that provide emergency food aid to disaster-struck countries.