Both firms are said to be suspending sales or discontinuing several crisp brands after Japan suffered its worst potato harvest in at least 34 years.
Typhoons and floods in Hokkaido, its main potato-growing region, last year caused a shortage of the vegetable.
Calbee looked to cover the shortfall by increasing US potato imports, but that proved insufficient to meet demand.
According to local media reports, including The Japan Times and The Manichi, Calbee and Koike-Ya are halting shipments of 49 potato crisp products.
Calbee, which owns more than half of Japan's snack food market, saw shares fell by more than 1% to a two-month low on Tuesday.
Koike-ya, which is Japan's second-largest snack maker, saw shares tumble by 3.5% on Tuesday.
Both companies declined to comment whether there would be an impact on their upcoming earnings.
Retail potato prices have been rising nearly 20% every month since last October, according to Japan's Ministry of Internal Affairs and Communications.
The higher prices are being felt in Tokyo, where 1kg of potatoes now costs 402 yen (Â£2.95; $3.60), compared with 336 yen in the same month a year ago, Reuters news agency said.
The agriculture ministry has been keeping records of harvests since 1983.
Japanese potato crisp-maker Calbee and its main rival Koike-Ya are facing a major crunch in their supply chain.