Andrew RT Davies has distanced himself from claims that favoured people are being imposed by the party centrally.
He said there should be "a slate" so local associations have a choice.
One regional official warned that the imposition of a candidate in Bridgend could cost the party one of its main target seats.
Karen Robson was named by the party centrally after activists asked for a "local" candidate to be added to a shortlist of two.
A general election candidate was also effectively imposed in Newport West - Angela Jones-Evans - where no other name was offered to activists.
Challenged on what happened in Newport West, Mr Davies told LBC radio at the weekend that he had "no part to play in candidate selection in Wales whatsoever".
He said such questions were better directed to the chairman of the party "who has been dealing with these matters in Wales" and that it was a "voluntary party matter".
But Mr Davies added: "Without a shadow of a doubt, in my opinion, it should be a slate of candidates so associations should have a choice."
However, the Welsh Tory leader said the Newport West selection had been made "with the agreement of the association" and denied it had been "imposed".
He said the constituency party had an "excellent candidate" in Ms Jones-Evans.
Welsh Conservative chairman Jonathan Evans has been asked to comment.
Tory party members should be able to choose between candidates standing for election, the leader of the Welsh Conservatives has said.