Better known by punk fans as Johnny Rotten, the band's frontman believes the May re-issue - to tie in with the monarch's Diamond Jubilee - "undermines" the band's original radicalism.
"I would like to very strongly distance myself from the recent stories and campaign to push 'God Save The Queen' for the number one spot," the singer told BBC News in a statement.
"I am proud of what The Sex Pistols achieved and always will be but this campaign totally undermines what The Sex Pistols stood for.
"This is not my campaign. I am pleased that the Sex Pistols recordings are being put out there for a new generation; however, I wish for no part in the circus that is being built up around it."
Originally released in 1977, the song coincided with the Queen's Silver Jubilee, causing uproar with lyrics, "God save the queen / She ain't no human being / And there's no future / In England's dreaming".
'God Save The Queen' is being put on sale again by Universal to celebrate the group's 35th anniversary, having previously been re-released in 2002 to mark the group's 25th year.
Listen to Sex Pistols' 'God Save The Queen' below: