It was announced on Tuesday morning that Cleverly would put his WBO light-heavyweight belt on the line against the Germany-based Serbian at the Royal Albert Hall on April 28.
But the WBO president Francisco Valcarcel reacted swiftly by claiming that having beaten Tommy Karpency last month, Cleverly must face a mandatory opponent.
"Francisco Valcarcel commented that the bout between Nathan Cleverly and Robin Krasniqi can't and won't be sanctioned," read a statement.
"Nathan Cleverly's fight with Karpency was sanctioned with the provision that the winner meet his mandatory opponent 120 days from the day of the bout."
A spokesman for Warren confirmed the promoter is in talks with the WBO in the hope of resolving the impasse.
Earlier, Cleverly spoke of the challenge posed by little-known Krasniqi and his delight at the prospect of boxing at the Royal Albert Hall.
The 25-year-old's proposed fourth title defence will be the first time a fight at that level has been staged at the Royal Albert Hall since 1995.
Twelve years ago the Welshman's compatriot Joe Calzaghe defeated Stephen Wilson at the famous London venue.
Krasniqi, 24, has won 37 of his 39 fights with both losses coming on points at the start of his career.
"Krasniqi's got a good record and he's bound to be a hard test for me," he said.
"The better the opponents the better I perform and Krasniqi will bring out the best in me.
"It's great to be the first boxer in over 10 years to open up the doors to the Royal Albert Hall again.
"It's a who's who of boxing who have fought at the Albert Hall and to add my name alongside greats like Lennox Lewis, Naseem Hamed, Nigel Benn and Joe Calzaghe is a real honour and dream."