Grain traders surveyed by The Wall Street Journal this week, for example, expected sales of old and new crop soybeans—soybeans harvested last year and those growing in the fields right now—of 300,000 metric tons to 1.25 million tons.

Instead, the USDA reported sales of more than 5 million tons of soybeans—a figure that struck many traders as ludicrous.

In Bloomington, Ill., Paul Dubravec questioned the numbers immediately.

“We’re still trying to figure out what the export report said yesterday,” said Mr. Dubravec, vice president of Advance Trading Inc., which advises farmers, grain-warehouse operators, food companies and others on hedging commodity prices. “Everyone’s just kind of scratching their heads right now.”

The USDA retracted the report after the close of trading Thursday. In a brief statement, the agency blamed the wild figures on the move to the new system.

“Today’s issues occurred despite the measures taken over many months to transition exporters to the new system and to ensure the accuracy of the data reported,” the agency said.

The USDA didn’t respond to requests for further comment on the apparent malfunction. As of Friday afternoon, it has yet to release an corrected version of the report.

Some traders were forgiving of the USDA’s misfire.

“OK, so they had a miscue—no one is perfect,” said Brian Pullam, an agricultural trader with Chicago-based company Linn & Associates. “Surely not I, as I would be sitting on a beach somewhere if I was.”

The timing of the transitions issues could have been better. This week, a crop tour hosted by Professional Farmers of America Inc. showed that the worst drought in at least a decade is inflicting pain on crops growing in the western Corn Belt.

Grain futures on the Chicago Board of Trade sold off Thursday in reaction to the seemingly unreliable figures. Continuous corn futures closed down 1.1%, soybeans closed down 1.8%, and wheat finished 3% lower. On Friday, they bounced back, with corn closing up for the day 2.3%, soybeans up 2.3%, and wheat up 2.8%.

Grain prices have climbed this week amid reports of drier-than-expected crops seen in the western Corn Belt during Pro Farmer’s crop tour as well as worsened drought conditions in China and the European Union.

The weekly report that was garbled Thursday normally shows total exports of a number of U.S. farm products from the preceding week, including corn, oats, soybeans and wheat. Traders and analysts use it to develop a picture of overall supply and demand in the agriculture markets.

Still, it isn’t as vital to agriculture as some other government data releases. That is because the USDA reports some large grain sales on a rolling basis. Private researchers also have other ways of gauging supply-and-demand factors in real time, such as gathering sales data from companies or even sending drones flying over farm fields.

The bungled report didn’t have a big impact on Wall Street either, since agricultural commodities account for a relatively small part of the investment allocations of large fund managers or macro hedge funds.

Some traders worried that further data hiccups could add uncertainty to an already turbulent market. Crop prices in some cases have hit records this year due to fighting in Ukraine, harsh weather and supply-chain issues.

“Markets hate uncertainty, and that was a lot of uncertainty,” said Jason Britt, president of Central States Commodities. “We all hope they get it straightened out.”

Write to Kirk Maltais at kirk.maltais@wsj.com and Alexander Osipovich at alexander.osipovich@wsj.com