“The FDA Food Safety Modernization Act is a common sense law that shifts the food safety focus from reactive to preventive,” Health and Human Services Secretary Kathleen Sebelius said in a statement. (Charles Dharapak/AP)

The Obama administration moved ahead Friday with the first major overhaul of the nation’s food-safety system in more than 70 years, proposing tough new standards for fruit and vegetable producers and food manufacturers.

The long-awaited proposals by the Food and Drug Administration are part of a fundamental change aimed at preventing food-borne outbreaks — caused by everything from leafy greens to cantaloupes to peanut butter — rather than simply reacting to them. Every year, contaminated foods sicken an estimated 48 million Americans and kill 3,000.

The rules, which span 1,200 pages, are aimed at creating safer conditions from farm to fork. Produce farmers would be required to ensure that their crops aren’t contaminated by bad water or animal waste. Some will likely be compelled to build fences to keep out wildlife and to provide adequate restrooms and hand-washing facilities for field workers.

Food-processing companies would be required to design and document an exhaustive regimen of sanitary measures — from pest control to bathroom cleanliness to what workers wear on the factory floor.

“It’s a big leap forward in applying modern, preventive measures across the whole food supply,” Michael R. Taylor, the FDA’s deputy commissioner for foods and veterinary medicine, said in an interview. “It’s important to see these rules as setting the standards for food safety.”

The proposed rules focus on two key portions of a broader food-safety bill that President Obama signed into law two years ago and that many lawmakers, consumer advocates and industry officials say has taken far too long to implement.

FDA officials and consumer advocates say the rules are essential to laying the groundwork for a major revamping of the country’s food safety system.

These rules “are the heart and soul of the law,” said Sandra Eskin, director of the Food Safety Campaign at the Pew Charitable Trusts. “These are the priorities. Everything else flows from them.”

Taylor said FDA officials tried to craft the rules in a way that would set a common safety standard while allowing for the different ways in which foods are produced.

“The strength of this system is it is science-based; it’s not one-size-fits-all. It’s inherently adaptable to all sorts of operations,” he said. “We’re looking to take widely recognized principles and apply them to a widely diverse food supply.”

Food industry groups welcomed the proposals, saying they provided some clarity but stopped short of endorsing them outright. They said many growers and processors already adhere to high standards. Groups such as the Grocery Manufacturers Association and the Produce Marketing Association said they would continue to work with the FDA to shape the rules in the months ahead.

The FDA estimated that the produce regulations would cost a large farm roughly $30,000 a year. The agency exempted a wide array of fruits and vegetables that are almost always consumed only after being cooked or canned, from plantains to pumpkins to sweet potatoes.

What remains unclear is how to pay for a wave of new inspectors and additional regulations, which the Congressional Budget Office estimated would cost the government $1.4 billion over the first five years.

FDA officials have said that they will rely in part on help from state and local governments, and Commissioner Margaret Hamburg has said that user fees from food companies and farms could help pay for the increased oversight costs. But Republicans in the House, eager to shrink the size of government and skeptical that the pending regulations warrant vast new resources, have resisted an increase in funds for the FDA.

“We still have a food supply that’s 99.99 percent safe,” Rep. Jack Kingston (R-Ga.) told The Washington Post shortly after Congress approved the food safety bill in late 2010. “No one wants anybody to get sick, and we should always strive to make sure food is safe. But the case for a $1.4 billion expenditure isn’t there.”

The next summer, House Republicans made much the same argument in voting to cut millions of dollars from the FDA’s budget, arguing that the greatest priority was reducing the budget deficit.

“We need additional resources to fully fund” the law, Taylor said when asked how the agency would pay for the new rules. “We’re hopeful we can work with Congress to get those resources.”

President Obama set the stage for a massive food-safety overhaul early in his presidency when he used a weekly address in March 2009 to highlight outbreaks involving spinach, peppers and peanut products that had sickened Americans in recent years. “Food safety is something I take seriously, not just as your president but as a parent,” he said.

Nearly two years later, Congress passed the far-reaching Food Safety Modernization Act with bipartisan support and backing from an array of consumer groups and food industry representatives.

The law focuses on the 80 percent of the food supply regulated by the Food and Drug Administration, including produce, dairy and seafood. Beef, poultry and some egg products are overseen by the Department of Agriculture.

The law gives the FDA broad new powers, including the ability to force companies to recall products and the authority to examine internal records at farms and food-production plants. It calls on the FDA to increase inspections, particularly at “high-risk” facilities prone to contamination, and to hire about 2,000 new inspectors.

Supporters had grown increasingly frustrated by repeated delays in the rule-writing process. Food safety experts, consumer groups, industry representatives, editorial boards and lawmakers on Capitol Hill took turns urging the Office of Management and Budget to release the rules.

Those calls grew louder after a 2011 outbreak of listeria traced to cantaloupe that left 33 people dead and led inspectors to unsanitary equipment at a processing plant in Colorado. In November, a salmonella outbreak that sickened 42 people in numerous states prompted the FDA to assert its new powers to temporarily halt production at the country’s largest organic peanut butter producer after finding numerous safety and sanitation problems.

The new proposals spent more than a year awaiting final approval from the OMB. That led some stakeholders to speculate that the administration might have been holding up the proposals until after the election.

“There’s no one explanation,” Taylor said when asked about the long delay. “They are complicated and interconnected; they are legitimately complex.”

More proposed rules are expected to be issued soon, including ones that would require that imported foods comply with U.S. safety standards. The FDA also plans to propose rules involving the production of animal foods.

It could be years before the proposals become final regulations. The FDA will take comments on the proposals for four months and then probably make changes. And some farms will have two years or more to comply with the rules.