WASHINGTON — An Indiana farmer who clashed with Monsanto Co. over his replanting of its patented soybean seeds ran into a steady stream of questions Tuesday from the Supreme Court.

At question in the patent dispute is whether Monsanto’s patent protection for its genetically modified seeds covers not just the first planting, but also seeds that are generated later.

To protect its investment, Monsanto has a policy that prohibits farmers from saving or reusing the seeds once the crop is grown. Farmers must buy new seeds every year.

“Why in the world” would any company invest millions of dollars in creating a new seed if a farmer could buy one and freely reproduce it, asked Chief Justice John Roberts.

Mark Walters, a lawyer representing Indiana farmer Hugh Bowman, argued that a patent holder “exhausts” his rights after selling the product.

He also argued that Monsanto has used patent law to bully farmers.

“What they are asking for is for the farmer to assume all the risk of farming, but yet they can sit back and control how that product is used,” Walters said.

But several justices said that made no sense for products that are easily copied, or in the case of seeds, copy themselves.

Justice Antonin Scalia said the farmer was free to use the seeds by planting a crop. But he can’t “grow additional seeds. It’s the other seeds we are talking about,” he said.

Justice Sonia Sotomayor echoed that thought. The patent law “doesn’t permit you to make another item. You can use the seed. But you can’t use its progeny,” she said.

The court’s decision to hear the case of Bowman v.Monsanto set off alarms in the biotechnology industry and among software makers. Those companies rely on strict enforcement of patent and copyright laws to protect their innovative products from being copied by others.

Bowman, a 75-year-old bachelor farmer, said he buys Monsanto’s popular and costly soybean seeds because they are engineered to withstand the spraying of herbicides to kill weeds. But for his second crop of the season, he tries to save money by buying soybeans from a local grain elevator. These seeds include a large percentage of Monsanto’s patented seeds, and the company sued him for violating its patent rights.

Lower courts ruled for Monsanto, but the Supreme Court agreed to hear Bowman’s claim that the seed maker had exhausted its patent rights when it sold its seeds.

An Obama administration lawyer joined sides with Monsanto in urging the court to reject Bowman’s claim.

“The exhaustion doctrine has nothing to do with this case,” Melissa Sherry, an assistant solicitor general, told the justices. Otherwise, a company’s 20-year patent protection would expire after “one and only one sale,” she said.

Washington attorney Seth Waxman, representing Monsanto, said the company had spent 13 years and hundreds of millions of dollars developing the herbicide-resistant seed at issue in the case. If Bowman’s claim were upheld, the value of Monsanto’s patented product would be gone “the very first time it sold a seed,” he said.

Information for this article was contributed by Mark Sherman of The Associated Press.

Front Section, Pages 2 on 02/20/2013