The chip is used in HTC's recently launched One XL phone and was due to be in future HTC and Nokia smartphones as well as tablet computers from Lenovo. Shortages could seriously delay deliveries of existing products.
More than 150 devices were due to be released with the Snapdragon S4 chip and other models of Snapdragon processors are also used in Blackberry and Nokia smartphones and Samsung tablets.
Apple will be unaffected by the shortage.
Qualcomm said that the factories where the processor is built would not be able to make enough of the S4 chip this year. It is trying to convince handset makers to use its other chips, but admitted that some may switch to other suppliers. This could have an effect on some smartphone prices.
The news emerged in a conference call to Qualcomm's investors from its chief operating officer Steve Mollenkopf. Shares in the chipmaker fell 7 per cent after the announcement.
Mollenkopf told investors: "We've been helping customers to see how they can swap in our Fusion 2 chipset... [but] we do expect to see some alternative non-Qualcomm chipsets used to solve that issue as well."
