A former Environmental Protection Agency employee pleaded not guilty in federal court Wednesday to charges that he fraudulently approved fuel products to benefit a company he secretly owned.

Prosecutors claim that Joseph Fernandes, a chemical engineer whose primary job was to sign off on new fuel additive registrations at the EPA, also owned a fuel company called Amtech. Court documents state that between 2001 and 2004, Fernandes had Amtech employees fill out applications for new fuel products, and he would approve the applications despite having a conflict of interest.

Fernandes had a financial stake in several products submitted to his office, according to his indictment. The products were then sold over the Internet and at automotive trade shows. Some of the applications also falsely stated that the products had already been tested, which expedited their approval.

As part of his job, Fernandes had high-level access to confidential information about the make up of fuel products, and court documents claim that he released this information illegally. 

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A grand jury indicted Fernandes in 2005 on charges of concealing material information and having a financial conflict of interest, but the charges were sealed because he was out of the country and authorities feared he would not return. An agent arrested him on May 27 as he walked off a plane from India.

Court documents state that Fernandes never revealed his conflict to the EPA. An agency spokesman Wednesday said he could not comment on the matter because it relates to confidential personnel issues and an ongoing court case.