The Daily Mail says Benjani is at the centre of a £7.6million transfer wrangle after he failed a medical.
The Barclays Premier League failed to reach a conclusion after a day of deliberation and Portsmouth and City are now at loggerheads.
City boss Sven Goran Eriksson maintains he wants to sign the Pompey striker but City officials are not convinced the player wants to move.
Benjani missed the 3.15pm flight from Eastleigh and then, to City's consternation, the next plane that left at 5pm.
The following flight to Manchester was cancelled before Benjani arrived on the delayed 8.50, reaching the Carrington complex at 11.10pm for a short, unsatisfactory medical.
Despite doubts over Benjani's commitment, City began faxing through documentation to the Premier League and triggered Jermain Defoe's £9m move from Tottenham to Fratton Park.
Pompey hoped to use the cash from Benjani's transfer to fund Defoe's move, but manager Harry Redknapp may now be forced to take him back if the legal wrangle cannot be resolved.
The Premier League are proposing arbitration and hope the clubs can iron out a reduced fee based on the medical.