The shortages were a milder repeat of last summer, when Apple’s stores quickly exhausted supplies of the then-new iPhone 3G, a situation that persisted for several weeks until the company could refill the pipeline.
On Sunday, Apple’s stock-checking tool indicated that 13 of the 211 stores in the US, or 6 percent of the total, were completely out of the iPhone 3GS.
Another 31 stores, or 15 percent, had only one of the four models for sale.
Apple revealed that it sold more than a million iPhone 3G S handsets over the first weekend of sales, despite the high cost of upgrading from previous models of the smartphone.
The figure exceeds that predicted by Piper Jaffray analyst Gene Munster, who thought 500,000 handsets would be sold.