The ministry estimates this season's crop at 50 million tonnes in the world's third-biggest soybean exporter.
Severe dryness late last year cut into soy output forecasts for Argentina but rains in January and February improved the outlook.
"The harvest continues at a good pace and with uneven yields depending on the area," the government said in its weekly crop report about Venado Tuerto in Santa Fe, the country's third largest soy producing province.
"Fortunately, it is better than expected."
By Thursday, growers had gathered 34 percent of the estimated area of 18.6 million hectares (46 million acres), up 13 percentage points from the prior week but lagging last season's pace by 8 points.
"Crops planted with early-season soy in Tres Arroyos varied depending on the amount of rainfall from regular to very good," the report said.
Tres Arroyos lies in Southern Buenos Aires province, Argentina's top soy-growing region.
The Buenos Aires Grains exchange hiked its for soy output to 49.2 million tonnes on Thursday, up from a previous estimate of 48.8 million tonnes.
The US Department of Agriculture (USDA) forecasts Argentina's soy crop at 49.5 million tonnes.
Argentina is the world's biggest exporter of soyoil and soymeal and a major wheat supplier.
The South American country is also the No. 2 corn provider after the United States and farmers are bringing in the 2010/11 crop, which the ministry forecasts at 20.8 million tonnes.
Gathering of this season's corn crop slowed this week as farmers made soy harvesting the priority, the government report said.
By Thursday, when the report is updated, farmers had brought in corn from 40 percent of harvestable lands, advancing 8 percentage points from the previous week but lagging 6 points behind last season's harvest pace.
The Buenos Aires Grains Exchange sees Argentine corn output at 20 million tonnes while the USDA foresees a crop of 22 million tonnes.
Argentine farmers have harvested 99 percent of sun-seed crop, which is expected to come in at 3.7 million tonnes.