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The company has expanded rapidly in the past decade through a series of mergers. At the beginning of 2004, it rolled out an SAP system to consolidate its legacy accounting systems.
The new package highlighted problems in CP Ships' accounting practices, which left a £23m gap in the company's accounts for the past two years.
CP Ships' chairman, Ray Mills, said last month, "The restatements are a major blow to the company, but our controls will be significantly improved with SAP."
Chief financial officer Ian Webber said SAP "has led to improved accounts reconciliation procedures and improved visibility of balances".
Five of the company's seven divisions are operating SAP and the the remainder will transfer by the first quarter of 2005.