Vaughan is convinced that if England continue with Cook in charge of their one-day international team they are doomed to failure when they take on the world in Australia and New Zealand in February and March.
Cook continues to be beset by increasing calls for his resignation, after leading England to three successive Royal London Series heavy defeats against India in the past week.
Former Test and ODI captain Vaughan wrote in his Daily Telegraph column, published online: "Cook is a stubborn man. He proved it this summer when he defied people calling for him to go and made his point by winning the Test series against India.
"But one-day cricket is different. If he is not going to stand down then the tough call has to be made."
Vaughan, a former Ashes-winning leader but - like all others for England - a World Cup loser, does not want history to repeat itself as it did in his playing days.
"Mike Atherton, Nasser Hussain, Andrew Strauss and myself thought we could do the job - but we were Test match cricketers and could not adapt," he added.
"Cook is cut from similar cloth and, at the moment, he is dropping players from the team who are better one-day cricketers than him.
"The captain is going up to players telling them they are not in the team - and they must be looking back wondering 'how are you still in it?'"
Vaughan advocates replacing Cook as captain with limited-overs specialist Eoin Morgan, and insists it is not too late for a rethink from England coach Peter Moores and his management colleagues.
"With six months to go, other teams are looking at this side and hoping that Cook remains as captain, and opens the batting at next year's World Cup - because they know if that happens England will not be a threat," Vaughan added.
"I am speaking out now because, with 13 games to go to the World Cup, there is time to make a difference."
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