WASHINGTON— Supreme Court justices appeared troubled Monday over whether to stop deals between pharmaceutical corporations and their generic drug competitors that the government says could keep cheaper forms of medicine from American consumers for longer periods of time.

Justices heard arguments from the Justice Department against what the government calls “pay-for-delay” deals or “reverse settlements.”

Such deals arise when generic companies file a challenge at the Food and Drug Administration to the patents that give brand-name drugs a 20-year monopoly. The generic drugmakers aim to prove the patent is flawed or otherwise invalid, so they can launch a generic version well before the patent ends.

Brand-name drugmakers then usually sue the generic companies, which sets up what could be years of expensive litigation. When the two sides aren’t certain who will win, they often reach a compromise deal that allows the generic company to sell its cheaper copycat drug in a few years — but years before the drug’s patent would expire. Often, that settlement comes with a sizable payment from the brand-name company to the generic drugmaker.

Drugmakers say the settlements protect their interests but also benefit consumers by bringing inexpensive copycat medicines to market years earlier than they would arrive in any case generic drugmakers took to trial and lost. But federal officials counter that such deals add billions to the drug bills of American patients and taxpayers

A study by RBC Capital Markets Corp. of 371 cases during 2000-09 found brand-name companies won 89 at trial compared to 82 won by generic drugmakers. Another 175 ended in settlement deals, and 25 were dropped.

The Obama administration, backed by consumer groups and the American Medical Association, wants the court to stop the deals because it says they profit the drug companies but harm consumers.

What if a brand-name drug company is making $100 million, and a generic drug company says its product will reduce that to $10 million, so both companies agree that the brand name company would give the generic company $25 million to stay off the market, asked Justice Elena Kagan. “It’s clear what’s going on here is that they’re splitting monopoly profits, and the person who’s going to be injured are all the consumers out there,” Kagan said.

But Justice Sonia Sotomayor said it may be going too far to make these deals illegal on their face, instead of making the government prove they are anticompetitive in court in each case. “It would seem to me that you have to bear the burden of proving that the payment for services or the value given was too high,” she told Stewart.