Congress is poised to scrap funding for the only program that consistently tests select vegetables and fruit for pathogens — an initiative that’s led to about 30 recalls since 2009.

The Agriculture Department, which runs the Microbiological Data Program, says getting rid of it is a necessary belt-tightening measure during tough fiscal times. USDA officials have suggested that the initiative would be a better fit for the Food and Drug Administration, which regulates vegetables and fruits. But that agency lacks the money needed to marshal more inspectors, and there’s no sign that the program will be moved there.

President Obama did not request funds for the 11-year-old program in his most recent budget, and the House and Senate did not include any in the agriculture spending bills they’ve crafted.

Meanwhile, evidence has been mounting for at least a decade that fresh vegetables and fruit are a major source of food-borne illness. Deadly outbreaks linked to spinach and cantaloupe in recent years only underscore the risks. Last year, the Centers for Disease Control and Prevention reported that vegetables that grow on vines and stalks ranked second on a list of foods linked to the most illnesses, topped only by fruits and nuts.

Consumer advocates say they’re outraged that the government would cut the program, which was funded at about $5 million last year. They suspect that industry pressure, not fiscal constraints, influenced the government’s decision.

“It’s a small sum of money in the government sense,” said David Plunkett, senior staff attorney for food safety at the Center for Science in the Public Interest. “For the government, it’s not even a rounding error.”

When the program was created in 2001, its purpose was to collect data on the prevalence of food-borne pathogens on produce by working with state-run laboratories. But as the states started identifying salmonella, E. coli and other pathogens, the findings were reported to the FDA. The ensuing recalls — 31 since 2009 — soured the industry on a program it initially supported.

Last year, a USDA advisory group made up of industry representatives urged Agriculture Secretary Tom Vilsack to stop using the program — which currently tests seven commodities, including cantaloupe, lettuce and spinach — as a way of initiating recalls.

The industry says the program is not designed to prevent food-borne illnesses and in fact doesn’t do so. The products are sampled by state laboratories close to the end of their shelf life, said David Gombas, a senior vice president at United Fresh Produce Association, an industry trade group. By the time the samples are collected and tested and the results are forwarded to the FDA, nearly all the produce is out of circulation by the time the FDA initiates a recall.

“It is not designed to get the product out of consumers’ hands,” Gombas said.

United Fresh Produce and the Produce Marketing Association, another major industry trade group, also say the program does not determine where the contamination occurred and therefore does not provide lessons to government or industry about better practices. The industry groups say they’d rather see the program at the FDA, which already does its own produce testing.

But an analysis by Food Safety News, an industry trade publication, found that the cash-strapped agency pulled on average 80 percent fewer fresh produce samples for testing from 2009 to 2012 than the program, which pulls roughly 15,000 samples or more a year.

Mike Taylor, the FDA’s deputy commissioner for foods, said the program was a solid source of information. “I’m not going to pretend we’re glad the program is going away . . . but there’s so much more that goes into ensuring the safety of produce.”

The House and Senate have yet to vote on the final agriculture spending bills.