The ministry will ensure that these food items are sold at "25 percent lower than the (prevailing) market price," Mohammed Ibrahim Abu Shadi said in a statement.
Fruit and vegetable prices have risen significantly in the past two months in a country where 40 percent of the population lives below the poverty line.
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Abu Shadi said inspectors were intensifying their monitoring of all the country's markets, and warned that those failing to comply with government-regulated prices would jail and fines.
The penalties would range from one to five years in prison and fines from 1,000 Egyptian pounds ($135/100 euros) to 5,000 pounds.
On Monday, the government had already given vendors a week to reduce what it said were "excessive and unjustified price rise" of these products and warned it would "regulate the prices" if they did not come down.