The three-year-old gelding was prominent in the betting for the big Newmarket handicap next week after winning his last two races.
But an autumn campaign has now been shelved after Kryptos was found to have had a "slight amount of heat in his near foreleg" on Friday evening.
Berry said in a statement posted on www.beverleyhousestables.com: "While this was only very slight, it made me concerned enough to seek a second opinion this morning from our vet David Dugdale of Newmarket Equine Hospital.
"While the horse is 100 per cent sound and is only showing minimal signs of any problem, David and I share the opinion that, while there is nothing there at present which ought to interfere with his racing career next year and beyond, it would be unwise to run him again this season because, as we have detected a slight warning sign, we might find that another race in the near future might cause some long-term damage.
"While it would be very tempting to run Kryptos next weekend in such a valuable race in which he would have such a good chance, no race is worth taking an unnecessary risk with a horse's long-term future and welfare.
"Consequently, after discussion with his owner, Tony Fordham, we have decided that Kryptos will begin his winter holiday straight away, rather than in another month's time."