With President Barak Obama signing the bill overhauling food safety in the U.S. for the first time since the Great Depression, there is another task waiting to be accomplished: finding enough money in the federal budget to pay for it. Funding the new legislation is just one of the challenges facing the federal government and the Food and Drug Administration, as they prepare to implement the Food Safety Modernization Act.

The legislation directs the F.D.A., working with a number of public and private partners, to build a new system of food safety oversight. The F.S.M.A. is focused on preventing food safety problems, including pathogens and other dangers that may make people ill. But before this may happen, there is one obstacle that is standing in the way – a lack of money to implement the new law. And there is some opposition in Congress to the amount of money needed to implement all the legislative provisions.

It is falling to industry groups who supported the new legislation, consumer groups and others to convince the new Congress it must provide additional funding to the F.D.A. for the F.S.M.A. to be enforced. It is a problem because the Republicans, who now control the House of Representatives, have a goal to reduce government spending. According to the Congressional Budget Office, the new food safety measures will cost the government approximately $1.4 billion during the first five years, including the hiring of an additional 2,000 food safety inspectors.

But according to a Georgetown University study last year, food-borne illnesses cost the U.S. $152 billion a year in lost productivity, medical costs and other expenses, not counting food industry costs when a product is recalled. With the concerns about food safety over the past few years, particularly concerns about how F.D.A. carries out food safety inspections and its other activities, it is difficult to believe the money for the new food safety program won’t be there.

What the F.S.M.A. sets in motion is a process to change the way the F.D.A. carries out its food safety responsibilities. Concerns have centered about how the F.D.A. does food inspections, compared to the U.S. Department of Agriculture and its activities. One of the goals of the legislation is to make F.D.A. food safety activities more closely aligned with how the U.S.D.A. carries out its food safety actions. Even with the changes coming from the new law, the two agencies will not be operating identically.

The F.D.A. has the responsibility for regulating about 80% of the food supply in the United States, although some of those activities are delegated to state agencies. The remainder of the food supply, including meat, poultry and some egg products, are under the control of the U.S.D.A., with a small part of those activities also carried out by state agriculture departments.

The two agencies operate in different ways, and will likely continue to do so. The F.D.A.’s responsibilities will be changed from reacting to food safety problems, like dealing with contaminated food after a food-borne illness is reported, to preventing outbreaks in the first place, which is what U.S.D.A. inspections are structured to do. But according to the Government Accountability Office, the F.D.A. has been going into food plants for inspection on the average of about every 10 years, although in some cases, the F.D.A. has visited plants more often, every two or three years, which is still not all that frequent. In contrast, U.S.D.A. inspectors are required to be in meat and poultry plants every day the plant is operating, while the plant is slaughtering or processing meat or poultry.

Making the two agencies more similar in operation will be quite a challenge. While the F.D.A. requires seafood plants under its inspection to use a hazard analysis critical control point (HACCP) system to prevent food safety problems, it will now require other food processors to develop similar plans to prevent contamination, and test the plans to make sure they work.

A major piece of the law gives the F.D.A. the power to require recalls, rather than asking food companies to recall suspected contaminated food voluntarily. The F.D.A. will also have access to records at food production facilities and farms. The law will require increased inspections of food processing operations and farms, but unlike U.S.D.A.-inspected meat and poultry plants, some very small facilities are exempted from the new law. It would also require the F.D.A. to visit “high risk” establishments, where there is more potential for adulteration, once every five years at first, and then once every three years – still not very often by U.S.D.A. standards. Importers would have to verify products from outside the United States meet American safety standards.

Because the new legislation allows the F.D.A. to require plants to recall, there are concerns that U.S.D.A.’s Food Safety and Inspection Service will eventually be forced to change its method of operation to require meat and poultry plants to require recalls as well, rather than asking plants to recall products. If this were to happen, it would be a major change in the way the U.S.D.A. regulates the poultry and meat industry, and may lead to additional regulatory changes in the future.

The author is Meat&Poultry’s Washington correspondent, a contributing editor and a feature writer based in Lancaster, Pa. Shire also works as a food safety consultant and writer for Shire & Associates LLC.