The Argentine agricultural ministry saw the country's soybean production at 56.0m tonnes, down from 58.8m tonnes last season.
Argentine soybean sowings were pressured by a change in government export tariff policy, which encouraged farmers to switch acres to corn and wheat, with dry weather hitting planting in the south.
But analysts are warning that more hectares could still be lost due to flooding.
US figures could get a revision
This week the Rosario Grain Exchange forecast the Argentine soybean crop at 52.5m tonnes, compared to the 56.8m tonnes seen a year ago.
And last week private analyst Informa trimmed its idea of the crop by 1.0m tonnes, to 55.0m tones.
These figures are all well behind the US Department of Agriculture forecast of a 57.0m tonnes, made in December, though that number could be revised in Thursday's US government supply and demand data.
"The weather in Argentina continues to be very erratic," said analyst Michael Cordonnier.
"While farmers in the core production regions of the country are struggling with heavy rains, flooding, hail and severe storms, the farmers and ranchers in the southern production areas are facing a prolonged drought and high temperatures that have resulted in wild fires."
This dry weather has affected soybean planting in the region, with the Buenos Aires Grain Exchange on last week lowering their forecast of the soybean planted area by 300,000 hectares, to 19.3m hectares.
"The reduction was due to drought in southern Buenos Aires that delayed the planting of the double crop soybeans until the planting window had already closed," noted Dr Cordonnier.
"The reduction did not include any soybeans that may be abandoned due to flooding or saturated conditions."
"Certainly there will be soybean acreage lost due to the flooding and the extent of the losses will depend on the weather over the next two weeksm," Dr Cordonnier said.
"If the saturated areas of central Argentina remain dry for the next two weeks, some of the flooded soybeans could be replanted," Dr Cordonnier said.
"If the saturated areas receive more rain over the next two weeks, a lot of the drowned out soybeans will not be replanted because the planting window will have already closed."
"Therefore, it is possible that an additional 300,000 hectares or more of soybeans could be lost due to the flooding and saturated conditions."
Combined with the acres lost to dryness, this could leave planted area some 3% down from initial estimates.
By William Clarke