A proposed settlement to long-running litigation over credit card fees could mean you could pay more at stores to use certain types of credit card, or even have your card rejected.

Visa and Mastercard have reached a deal with merchants to settle a lawsuit that was filed in 2005 over the “swipe fees” that stores pay to credit card issuers – typically a little more than 2 percent of every purchase made with a card.

“Both sides worked in good faith to reach this new, comprehensive agreement,” the executive chairman of the Electronic Payments Coalition, Richard Hunt, said in a statement.

“It provides businesses of all sizes with meaningful and significant concessions that give more flexibility and choice in card acceptance.”

Mr. Hunt, whose organization represents the credit card issuers and processors, says the agreement offers retailers greater flexibility to pass along card processing costs, a more than 25 percent reduction in the fees they pay on standard credit cards, and a cap on the rates they will pay in future.

The deal breaks credit cards into three categories — commercial, premium consumer, and standard consumer. At present, the credit card companies require merchants that accept any of their cards to accept all of them, even though they charge a higher swipe fee on premium cards, such as those that provide air miles or other rewards.

Under the agreement, merchants would be allowed for the first time to charge customers more when they use premium cards or refuse to accept those cards altogether.

An analyst at Keffe, Bruyette, & Woods who covers the credit card industry, Sanjay Sakhrani, said in a note to clients that he doesn’t expect the settlement to have a far-reaching effect on credit card reward programs.

“Even if given the option to turn away certain cards, we see few merchants actually doing so given the implications it would have on the customer experience and the merchants’ sales,” Mr. Sakhrani stated.

The current proposal is the third attempt at a settlement and at least two groups that represent merchants say the federal judge overseeing the case should reject the deal.

“This proposal is all window dressing and no substance,” the general counsel for the National Retail Federation, Stephanie Martz, said in a statement. “The reduction in swipe fees doesn’t begin to go far enough, and the change in the honor-all-cards rule would accomplish nothing.”

Another group that represents merchants says the card industry is trying to get legal protection while offering little in return to merchants.

While the credit card industry says the agreement would cut overall costs to retailers by 25 percent over time, the retailers say the deal would shave only 0.1 percent off the current swipe fee, which averaged 2.35 percent last year.

They also say the cap on future fee increases applies only to the issuing banks, not to the credit card companies like Visa and Mastercard, which share the swipe fee proceeds.

“The miniscule reduction proposed in the settlement on bank fees could still allow Visa and Mastercard to be able to raise their own fees without any limits,” executive committee member of the Merchants Payment Coalition, Jennifer Hatcher, said in a statement.

“All of the supposed merchant and consumer savings could easily be canceled by Visa and Mastercard increasing their fees.”

The merchants coalition says swipe fees are often their highest operating cost after labor and lead to higher prices for consumers.

Total revenue from swipe fees for Visa and Mastercard credit cards has quadrupled since 2010 to reach $111.2 billion last year, according to the group.

The coalition claims the average American family pays nearly $1,200 a year in higher prices to cover swipe fees and says Congress needs to step in to fix the “broken” payments system.

Congress has considered but not passed the Credit Card Competition Act — an effort to inject competition into the system. Under the bill, merchants could submit charges on credit cards issued by large banks to their choice of more than one network, such as Visa or Mastercard, seeking the best rate.

Supporters of the legislation — sponsored by Senator Dick Durbin — claim it could save merchants and consumers $17 billion a year.The Electronic Payments Coalition, though, claims that credit card rewards would be “substantially reduced” if Mr. Durbin’s legislation passes.