The Kazakh champions courted controversy ahead of the first leg of their UEFA Champions League play-off against Celtic when they performed a ritual killing of a sheep the day before the clash.
The practice led to outrage from leading animal rights groups, with People for the Ethical Treatment of Animals (PETA) writing an open letter to UEFA president Michel Platini demanding action.
And European football's governing body has now responded to those concerns, threatening disciplinary proceedings should the practice be repeated.
Ahead of the second leg of the tie against Celtic on Wednesday night, which Shakhter lead 2-0, a letter to the club's executive director Yerden Khalilin was released to the press.
In it, UEFA competitions director Giorgio Marchetti wrote: "We were informed that an animal slaughter took place at some point prior to the UEFA Champions League fixture involving FC Shakhter Karagandy and Celtic FC at the Astana Arena on Tuesday 20 August 2013.
"Although certain practices may be culturally rooted, they have no place in or around a sporting arena or event.
"In this context, I would like to make you aware that animal slaughter on a football pitch or in a stadium before, during or after a UEFA competition match - or with reference to a UEFA competition - is totally improper, and will not be tolerated.
"In case of re-occurrence, it will inevitably lead to a full investigation by our disciplinary bodies."
