U.S. Food and Drug Administration Commissioner Margaret Hamburg Thursday warned of more outbreaks and import problems if food safety is not properly funded and defended a proposal to collect registration fees to help pay for oversight.

During a House appropriations hearing on the FDA’s budget, which is increasingly supplemented by fees aimed at drug makers, lawmakers questioned Hamburg about whether her agency would have enough resources to implement the sweeping Food Safety Modernization Act.

Rep. Sam Farr (D-CA), who represents Salinas, known as “America’s salad bowl” for it’s extensive fruit and vegetable production, asked the commissioner what would happen if FDA fails to get increased funding for food safety.

“It’s an enormous concern,” said Hamburg. “If we don’t get the money, we will see more foodborne outbreaks, we will not be able to work with companies to put in place the kind of systems we know make a difference.”

“We know that we’ll have increasing problems with food imports that don’t meet our standards and can’t be adequately screened. We know that more problems are going to happen. We have an opportunity to get in front of the problems and address them.”

“We are not, as a nation, putting the resources into food safety as we should be,” added Hamburg. “If you look at the budget…  if you look at how much every American is paying for the FDA, around food safety, it’s about three and a half dollars per year. If you look at the benefits we provide, I think it’s worth more than that.”

The most heated exchange of the hearing was over an Obama administration plan that proposed raising $220 million for food safety funding with food facility registration fees.  Appropriators pointed out that similar proposals had failed in the past, which raises concerns about whether FDA will see a real increase in resources for fiscal year 2013.

Rep. Tom Latham (R-IA) sharply questioned Hamburg on the proposal, arguing that it was simply a food tax that will fall on consumers.

“Is this food safety fee really needed? I would argue, emphatically, yes,” said Hamburg. “Food safety is of upmost importance to both consumers and to the food industry. We know that although we have one of the safest food supplies in the world but we still have some real vulnerabilities.”

Hamburg pointed to foodborne illness statistics and “a pretty dramatic” lack of consumer confidence in food safety. “It’s a wise investment that will pay off dividends down the road that will be dramatic,” she said.

“This is not a user fee, this is an existence fee,” said Latham, noting that FSMA did not explicitly authorize registration fees. “I just don’t understand what vehicle you’re going to use to authorize this fee.

“Why don’t you just ask for money rather than do something you know is not going to happen?” Latham asked.

“Well, if you want to give us the appropriations we’d be glad to have that,” said Hamburg, adding that she believed the registration fees were “an appropriate cost of doing business” and pointed out that drug companies also pay registration fees.

Using the same points raised by the 33 food industry groups who recently wrote to the subcommittee, Latham continued to press the issue: “You understand this has been rejected twice by Congress?”

“I am concerned about that,” said Hamburg. The exchange continued for several minutes.

Later in the hearing, Rep. Rosa DeLauro (D-CT), former chair of the subcommittee, ardently made the case for granting FDA regular appropriations.

“We could increase the budget authority!” she exclaimed, incredulously. “Quite frankly. I’m appalled with what the budget provides for food safety… I believe this is an abdication of our Congressional responsibility.”

“Those fees are not going to be approved. Without that where do you go?”

If FDA were able to pursue a registration fee, Hamburg did give some hint as to what the fee might look like.

“It would most likely be a fee that would very much reflect a number of important factors, including size of the company, levels of production, etc,” said Hamburg. “What we would hope to be doing is what we’ve done successfully with drugs and devices where we sit at the table with industry and the different components of the food system…and identify what are our goals? Where are the gaps? How can we best address them?”