"We've got some really good [systems] in the road map," Jacobs said. "We're making the investments needed to improve the supply."

The S4 is based on the ARM architecture and includes a 3G/4G radio and graphics cores. Microsoft is working with Qualcomm, Nvidia and Texas Instruments to make Windows on ARM devices.

The shortage of S4 chips may have a small impact on the prices of smartphones and tablets, and it may also affect Qualcomm's launch of Windows on ARM devices, said Nathan Brookwood, principal analyst at Insight 64.

Qualcomm may shift some S4 chips intended for phones toward tablets, or vice versa, depending on demand. But the shortage is a sign that S4 chips are in demand, which is good news.

The shortage has forced some Qualcomm licensees to look at S4 alternatives, Mollenkopf said. Some of Qualcomm's competitors include Nvidia, which offers the Tegra 3 processor, and Texas Instruments, with its OMAP chips. Qualcomm expects supply to be constrained until the December quarter and to become normal by next year.