LAHAINA, Hawaii — Trade negotiators from the United States and 11 other Pacific nations were headed toward failure Friday, with difficult talks on the largest regional trade agreement ever breaking down over protections for pharmaceutical companies and access to agriculture markets on both sides of the Pacific.

Negotiators will return to their home countries to obtain high-level signoffs for a small number of final sticking points on the agreement, the Trans-Pacific Partnership, with bilateral talks reconvening soon.

But the breakdown is a setback for the Obama administration, which had promoted the talks here as the final round ahead of an accord that would bind 40 percent of the world’s economy under a new set of rules for commerce.

President Obama’s trade push had been buoyed by Congress’s narrow passage in June of “fast track” trade negotiating powers, and American negotiators had hoped other countries could come together once Congress had given up the right to amend any final agreement.

In the end, a deal filled with 21st-century policies on Internet access, advanced pharmaceuticals, and clean energy trade foundered on issues that have bedeviled international trade for decades: access to dairy markets in Canada, sugar markets in the United States and rice markets in Japan.

Australia, Chile and New Zealand also continue to resist the United States push to protect the intellectual property of major pharmaceutical companies for as much as 12 years, shielding them from generic competition as they recoup the cost of developing next-generation “biologic” medicines.

“There’s always been more than one issue,” said Representative Sander Levin, Democrat of Michigan, who is here as an observer.

The trade ministers who gathered at the luxury hotels of Maui this week for talks that went deep into the night did have some successes. They reached agreement on broad environmental protections for some of the most sensitive, diverse and threatened ecosystems on Earth, closing one of the most contentious chapters of the Pacific accord.

They also reached agreement on how to label exports with distinct “geographic indications,” such as whether sparkling wine can be called champagne. And they agreed on a code of conduct and rules against conflicts of interest for arbitrators who would serve on extrajudicial tribunals to hear complaints from companies about whether their investments were unfairly damaged by government actions.

But the failure to complete the deal — eight years in the making — means the next round of negotiations will push the United States ratification fight into 2016, a presidential election year. Most Republican candidates are likely to back it, but a final agreement would force the Democratic front-runner Hillary Rodham Clinton to declare her position, which she has avoided.

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