"Along the banks of the Hernad, Sajo and Boldva rivers some 2 300 people were evacuated due to the water flooding homes in the towns and villages" in the northeast region, a spokesperson for the rescue services said.
Over 12 000 police officers, soldiers and firemen are involved in the rescue operation, which has enjoyed a rare dry spell since Friday that is forecast to last for the next week.
In Budapest the docks of the flooded river Danube were shut and the banks of Margaret island, a major tourist destination in the capital, were protected by sand bags.
Agriculture has been hit by the incessant rainfall too, with experts predicting a drop of between 30% and 40% in fruit production.
In the month of May alone, between 210mm and 220mm of rain fell per square metre, the equivalent of an entire year's worth of rainfall normally, according to meteorological services.
In northeastern Hungary, the level reached a record 273mm per square metre.