Clattenburg was due to take charge of Sunday's FA Community Shield clash between Manchester United and Portsmouth, but has now been replaced by Peter Walton.
A joint statement from the Football Association and the Professional Game Match Officials Ltd read: "PGMO is aware of media reports concerning alleged debts incurred by companies connected to referee Mark Clattenburg.
"It has been decided he will not officiate any matches pending enquiries into the background to these reports.
"The FA has also decided to appoint Peter Walton as referee for Sunday's FA Community Shield between Manchester United and Portsmouth in place of Mark Clattenburg."
A PGMO spokesman added: "It is in the best interests of Mark Clattenburg and the game that these reports are fully investigated and, during that time, he will not referee any matches.
"Mark Clattenburg is one of England's leading referees and we hope to resolve this matter swiftly."