About 1.5 million O2 customers transferred to the Companion system have received incomplete bills, and others have not received regular itemised bills since being transferred.
When BT Cellnet was re-branded as O2 after being sold off by BT three years ago, the new company inherited a jumble of billing systems serving different types of customers - pre-pay, contract, business and wholesale.
It decided to consolidate its legacy systems onto a single CRM platform supported by an integrated billing system serving all customers. An O2 spokesman described the migration as "one of the biggest IT projects in Europe".
Migration to the Companion system is being managed by IBM Global Services. IBM would not comment on problems with the system, but O2 said it was unable to print the number of free minutes on bills for the 1.5 million customers transferred to the new system.
O2 also said some customers had only received a bill summary, rather than an itemised bill. "There is an intermittent problem with a very small proportion of our customers who receive hard copies of our itemised bills," a company spokesman said.
In a letter to customers affected by the problem, O2 said, "We experienced a major system fault in July and August and there has been an error in the production of voice call charges.
"Our IT billing department has estimated that the issue will be resolved in October."