"We have reached a point where the win-at-all-cost approach of UK Sport has had its time," he told the Guardian on Friday.
"There is too much of a culture of medal winners and non-medal winners which is unhealthy and doesn’t speak well for us as a sporting society."
London is hosting the world athletics championships in August and Warner is the most outspoken senior figure so far to criticise the body that distributes government and National Lottery funding to sport in Britain.
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UK Sport's ruthless approach has produced record returns, with Britain second in the medals table at last year's Rio Olympics with 27 gold medals and 67 in total, but also caused controversy.
British cycling has been engulfed by allegations of bullying and sexism, with former performance director Dave Brailsford defending the organisation as "medallist" and meritocratic.
UK Sport's chief executive Liz Nicholl has said the latest round of funding leading up to the 2020 Tokyo Olympics is "uncompromisingly focussed on excellence, relative merit and what it takes to pursue the ambition to win more medals and create more medallists in Tokyo to inspire the nation".
That has meant sports such as badminton, basketball and wheelchair rugby missing out.
Warner hoped it was not too late for "a more elegant and intelligent objective than a pure medal-winning yardstick" and a rethink of some decisions.
"That might lead to some sports that are being disenfranchised still being able to be included in Tokyo funding," he added.
"Nothing would give a lot of people, including me, greater pleasure than seeing some of the sports that had their funding chopped go to Tokyo and win medals – and be able to stick a metaphorical finger up at those who say right now that they don’t have any chances."
(Reporting by Alan Baldwin; Editing by Alison Williams)
