"Each time the media uses the phrase 'swine flu,' a hog farmer, their workers and their families suffer," Vilsack said in a statement.
"It is simply not fair or correct to associate the 2009 pandemic H1N1 influenza with hogs, an animal that does not play a role in the ongoing transmission of the pandemic strain," he said.
When the new strain of flu was first reported in North America in April, even the global health authorities referred to the illness as swine flu.
But after the name led to several countries banning imports of pork or live swine from the United States, Canada and Mexico, where the outbreak was worst early on, the World Health Organization reexamined the nomenclature and began calling the virus influenza A(H1N1).
But the old, unflattering name has stuck and is hurting pig farmers.
According to Dave Warner, a spokesman for the US National Pork Producers Council, the US pork industry was "heading in the right direction" when the World Health Organization reported an outbreak of a new strain of flu in Mexico in late April.
The industry had weathered a tough 2007, when high grain and transportation prices meant farmers were losing 40 dollars per pig.
"But on April 24, hog futures prices were looking good. It looked like we would be seeing profits by about now," Warner told AFP.
"Farmers could see light at the end of the tunnel. We were headed in the right direction and about to enter the summer grilling season where pork sales traditionally go up. But H1N1 essentially wiped out all of that," he said.
From late April until mid-August, US pork producers saw their losses per head of stock nearly triple, to around 25 dollars per pig from less than 10 dollars.
The industry as a whole lost 991 million dollars during those four months, said Warner.
"At least half of that loss is attributable to H1N1 being called swine flu," he said.
More than 3,000 people have died of A(H1N1) flu since April. None contracted the viral illness from eating pork.