An outside audit has found that Metro violated federal contracting rules when it awarded a contract to a McLean information technology company, the latest controversy surrounding the more than $12 million contract.

The audit, from CliftonLarsonAllen, found that the agency's contract with Metaformers "did not follow federal procurement compliance requirements with respect to open competitive bids," according to a presentation that the firm is scheduled to make to board members Thursday. Metro hired the firm to audit its books as part of an annual review.

The auditors also found problems with work done as part of the project, including inconsistencies in documentation, the presentation says. They also said Metro relied on the contractor to control some of the system's security, which should have be handled internally.

The problems are the latest red flags about the contract, which was intended to help integrate two systems that Metro uses to track its financial systems and its business processes. The Department of Transportation's Inspector General's Office also is investigating the contract that received $5 million in federal stimulus funding, as The Washington Examiner first reported. It subpoenaed documents on the contract this summer.

The Metaformers contract, which cost at least $12.4 million, was awarded in June 2010 for a two-year period for $9.15 million, according to contract documents obtained byThe Washington Examiner. In April 2011, the contract amount was increased to $9.79 million. And in July 2011, Metro exercised another option, bringing the total to $12.4 million.

It was not immediately clear in what way Metro failed to follow the rules for bidding the contract. Federal contracting rules generally require bids for contracts to be done openly and include more than one bidder so that agencies cannot give a contract to a company without opening up the chance to other firms.

Metro declined to provide a copy of the audit or comment upon it. Metro spokeswoman Caroline Lukas said the agency does not yet have a copy of it, even though the agency submitted a management response to it and commissioned the reports.

Metaformers did not respond to a request for comment Tuesday.