The Bristol player has been told he faces eight weeks on the sidelines due to a wrist injury.
England boss Andy Robinson is still pondering his squad for next month's tour of Australia, but Perry was not one of the players thought to be in danger of missing out.
Perry, 28, said: "I'm gutted, as you can imagine.
"Touring with England would have been a dream come true and capped an amazing season. But the wrist wasn't right so it's important to get it sorted.
"I'm just looking forward now to getting fit, having a good pre-season and getting stuck into 2006-7 with Bristol.
"If I'm fit and performing well enough then hopefully I can force my way back into the England reckoning for the autumn internationals."
Tests on Perry's wrist revealed the injury had proven more serious than was feared when the former Coventry player sustained the blow, during April.
Bristol physiotherapist Paul Tompkins revealed: "Shaun did it against Newcastle Falcons when he collided with some advertising hoardings towards the end of the game.
"We did a x-ray the following day and a scan a week or so later but nothing showed up.
"However, it wasn't settling down so we spoke to the England Rugby team doctor Simon Kemp who referred Shaun to a specialist who carried out an MRI which showed up a fracture to his scaphoid."
Perry had seemed almost certain to win his first Test cap after an impressive campaign with Bristol, with his club boss Richard Hill supporting his claims for a call-up.
However, the untimely development means he faces a frustrating summer.
Tompkins added: "Shaun's seeing a specialist on Friday and will likely undergo surgery on Monday which will rule him out of contact for at least eight weeks."