The seven-time Wimbledon champion wore the shoes in his opening round win over Victor Hanescu on Monday.
But officials from the All England Lawn Tennis and Croquet Club have told him to bin them when he returns to centre court later on Wednesday to face Sergiy Stakhovsky.
"Players at Wimbledon must be dressed almost entirely in white," a spokesman told the Daily Telegraph.
Despite being a member of the All England Club, defending champion Federer is still expected to abide by the rules.
The world Number 3, who is chasing a record eighth title, has a specially-designed outfit provided for him each year by clothing giant Nike.