The shortages were a milder repeat of last summer, when Apple's stores quickly of the then-new iPhone 3G, a situation that until the company could refill the pipeline.
On Sunday, Apple's indicated that 13 of the 211 stores in the U.S., or 6% of the total, were completely out of the iPhone 3GS.
Another 31 stores, or 15%, had only one of the four models for sale.
The hardest-to-find iPhone 3GS was the $199 white 16GB model, which was out of stock in 121 stores, or 57% of the outlets. Supplies of the $299 32GB black iPhone 3GS were also short, as 84 stores, or 40% of the total, reported it unavailable.
Customers Sunday were most likely to find the $199 black 16GB iPhone 3GS and the $299 white 32GB model in stock: Just 23% of the stores were out of either of those configurations.