Based on a tip-off, the officials raided the Afghan Chappal House in the city's Namak Mandi area, the Dawn report said.
The shop's owner, Nooruddin Shinwari, in his defence said that the snakeskin had been sent from the US to the shop to craft two pairs of the 'Kaptaan Chappal', one for the donor and the other for Khan.
But District Forest Officer Wildlife Aleem Khan told Dawn news on Sunday that the Wildlife Department will on Monday begin a verification process for the confiscated shoe material.
Khyber Pakhtunkhwa's Minister for Environment Ishtiaq Urmur said making sandals from snakeskin was illegal.
"No matter who the sandals were being made for, an illegal act would never be tolerated.
"If it is proven that the chappals were indeed made of snakeskin then the cobbler will have to face legal consequences as well as a fine provided he shows necessary documentation that it was (legally) imported," he told Dawn news on Sunday.
In 2015, the traditional Peshawari chappal was launched by Nooruddin as Kaptaan Chappal.
"The special double-soled Peshawari chappal had been in fashion since long but when I gifted a pair of this especially designed new brand to Pakistan Tehreek-i-Insaf leader Imran Khan on his wedding, the shoe became an instant favourite with all," Nooruddin had told Dawn then.
( With inputs from IANS )