The flooding estimate — two to three million acres [about 0.8 to 1.2 million hectares] — was part of the Agriculture Ministry's weekly crop report on Thursday.
Across the province, topsoil moisture on cropland is rated as 34 per cent surplus, 64 per cent adequate and two per cent short.
As much as 200 millimetres of rain fell on parts of southeastern Saskatchewan June 27-30, flooding both rural and urban areas.
Basements were filled with water, sewer systems backed up and many farms were inundated.
Premier Brad Wall said earlier this month the damage done would likely exceed the $360 million spent following the 2011 flood. However, that figure did not include agricultural losses.
In the spring, Statistics Canada said Saskatchewan farmers intended to plant 35.3 million acres. Three million flooded acres would represent about 8 per cent of that.