More U.S. consumers are buying iPhones from third-party retailers instead of directly from Apple Inc., according to a new report, a shift that could cut into the tech giant's wide profit margins.

Consumer Intelligence Research Partners said 11% of U.S. iPhone buyers purchased phones directly from Apple in 2015, down from 16% two years earlier. Meantime, the share of U.S. iPhones bought at stores and websites operated by wireless carriers rose to 76% from 65% over the period. The remaining phones were purchased from other retailers, such as Best Buy Co.

That shift is generally bad news for Apple, which keeps more profit from selling products directly than via third parties, analysts said. In its stores, Apple also can better control the customer experience and prevent shoppers from choosing another brand.

"Apple makes higher margins selling direct than through third-party retailers because it has to pay them a cut," said technology analyst Jan Dawson, founder of Jackdaw Research LLC. At stores that sell a variety of smartphones -- many offering similar features as iPhones at lower prices -- "there's a risk of customers coming in wanting an iPhone and walking out with something else."

But the impact on Apple's bottom line is likely slight, analysts said. Apple sold roughly 50% more iPhones world-wide in 2015, compared with 2013, suggesting that the number of phones bought directly from Apple increased, though not as fast as the number bought elsewhere.

Moreover, some analysts said Apple benefits overall from a stronger ecosystem supporting its devices.

"Historically in the tech space, large vendors do very well but the ecosystem doesn't," said Abhey Lamba, an analyst at Mizuho Securities Co. "In the long run, this is good" for Apple.

An Apple spokeswoman declined to comment.

IPhone buyers are shifting away from Apple stores as wireless carriers offer to upgrade phones more quickly than in the past, and offer more installment plans and leasing options. For example, Sprint Corp. offers to lease an iPhone 6S for $1 a month, with the trade-in of a previous generation iPhone 6. T-Mobile offers a similar plan for $5 a month.

Apple unveiled its own iPhone leasing plan in September, which costs about $32 a month for the basic 16 GB iPhone 6S, including its AppleCare+ protection service.

Wireless carriers' stores are also becoming a more popular place to buy iPads as carriers pitch data plans for tablet computers. Carriers sold 18% of iPads in the U.S. in 2015, compared with 6% two years earlier, according to the Consumer Intelligence data. Apple stores' share of U.S. iPad sales held roughly steady at 23% over the period. The carriers gained share from Best Buy and Amazon.com Inc.

Apple stores still dominate sales of Mac computers, accounting for 44% of all U.S. Mac purchases last year. Best Buy had the next largest share at about 20%.

Analysts said the relatively small number of Apple stores -- 267 in the U.S. -- compared with thousands of wireless-carrier locations, means many consumers outside of cities will continue to purchase devices from third parties.

"People like to see these things in person, and if you're going to a local carrier store, why not buy it right there?" Mr. Dawson said.

There have also been other recent troubling signs for Apple stores. Shopping-mall operator General Growth Properties said holiday-season sales at Apple stores were disappointing. General Growth CEO Sandeep Mathrani told analysts in February that fourth-quarter sales per square foot in non-department stores increased in nearly every major retail category except for electronics, "primarily due to Apple."

The Consumer Intelligence report offers a rare glimpse of Apple's retail operations amid fewer disclosures about the business. Apple recently stopped breaking out revenue from its retail operations in earnings statements.

Apple opened its first store in 2001. The stores were meant to showcase Apple's Mac computers, away from the crush at other electronics retailers. The stores have become a physical manifestation of what Apple hopes to convey with its products: beautiful, comfortable and hassle-free.

Consumer Intelligence co-founder Michael Levin estimated that about two-thirds of Apple's U.S. retail sales come from its brick-and-mortar stores and one-third from its online store.

Since Apple tapped former Burberry Group PLC Chief Executive Angela Ahrendts as its retail chief in 2014, the company has steadily opened new stores, with a particular focus in China and other emerging markets. Ms. Ahrendts has also sought to integrate Apple's online and physical presence, allowing customers to buy phones online and pick them up in stores, for example.

Apple is also now dedicating more of its prime shelf space to its own accessories. These days, the company puts the vast array of Apple-branded iPhone cases on its prime wall space in most Apple stores, while displaying third-party cases in less prominent locations.

Write to Daisuke Wakabayashi at Daisuke.Wakabayashi@wsj.com and Jack Nicas at jack.nicas@wsj.com