In its news release on the recall, the agency asserted that Rancho "processed diseased and unsound animals" without a full inspection. The meat products are "unsound, unwholesome or otherwise are unfit for human food" and must be removed from commerce.
There are no reports of anyone becoming ill after eating the beef.
The involvement of the inspector general's office suggests a more serious level of inquiry by the USDA, one expert said.
The Office of the Inspector General "doesn't get involved in every case," said Michael Hansen, a senior scientist who follows the meat processing industry for Consumer's Union, the policy and advocacy division of Consumer Reports magazine. "That suggests that something else is going on that needs to be looked at."
However, a spokesman for a national meat processors group said Tuesday's statement simply confirmed what was already known, namely that an investigation was underway.
The Office of the Inspector General is the investigative arm of the USDA, said Jeremy Russell, director of communications and government relations in Oakland for the North American Meat Association. Its involvement, he said, merely suggests "there was some practice that the USDA feels it needs to investigate."
The department's concerns about Rancho first came to light Jan. 10 when federal agents and Petaluma police converged on the Petaluma Boulevard North plant.
Three days later the USDA announced that Rancho was recalling 41,683 pounds of meat it had processed on Jan. 8. The agency asserted the meat didn't receive a full federal inspection.
On Saturday that recall was expanded to all beef processed at Rancho between Jan. 1, 2013, and Jan. 7, 2014, a USDA spokesman said. The recall involves both the carcasses, the finished bodies of the animals, and the other parts, commonly referred to as offal.
The processed beef was shipped to retailers and distributors in California, Florida, Illinois and Texas, according to the announcement. The USDA released the names of 14 stores in Sonoma, Napa and Marin counties that have been instructed to return meat processed by Rancho. Five were markets that cater to Latino customers.
Other than the two recall announcements and the statement on Tuesday, USDA officials have declined to elaborate on the underlying reasons for the recall or the breadth of their investigation.
Similarly, the plant's owners, Robert Singleton and Jesse "Babe" Amaral, have limited their comments to a confirmation Monday that Rancho had voluntarily ceased processing and was compiling a list of affected companies.
At that time, Singleton said the company undertook the recall out of "an abundance of caution" but declined comment on the government's allegations. Both men were unavailable Tuesday.
Even as the government and the owners say little, North Bay ranchers and meat processors continue to raise concerns about the impact of the closure and the possible loss of a key facility for the region's cattle industry.
"We are outraged, absolutely outraged by the closure," said Lesley Brabyn, owner of Salmon Creek Ranch between Bodega and Bodega Bay. "They're going to put all small farmers who are trying to humanely raise animals out of business."
Brabyn said ranchers can make $5,000 from each steer processed at Rancho. She would normally take 25 to 30 steers there each year. Transporting those animals to processors three hours away will raise ranchers' costs significantly, she said.