Argentina is the world's No. 3 soybean supplier and its top exporter of soyoil and soymeal. A lack of rain has driven global prices higher although recent showers have brought some relief.
"Despite the good volume of precipitation accumulated in much of the farming region during the last 15 days, there are still areas that do not have adequate soil moisture," the Buenos Aires Grains Exchange said in its weekly report.
"Much of the central farming region registered losses to its potential yields ... during the prolonged period of dry weather and high temperatures that began in early January and lasted until mid-February," the exchange said.
A soy crop of 48.5 million tonnes would still represent a 21.6 percent increase from last season, when drought hit production hard.
"Nonetheless, this new production estimate is still subject to future climate conditions - rains during the coming months and the first frosts of the year - to sustain the yield potential we estimate currently," the exchange said.
Regarding 2012/13 corn output, the exchange held its estimate for a record 25 million tonnes and said the crop had benefited in many areas from rain and lower temperatures.
It also said farmers have harvested 6 percent of commercial-use corn to date.
The Rosario grains exchange slashed its soybean production estimate this week to 48 million tonnes and trimmed its outlook for 2012/13 corn to 25.5 million tonnes.
Meanwhile, the US Department of Agriculture forecasts Argentina's 2012/13 soy output at 53 million tonnes, and corn production at 27 million tonnes.