LAFAYETTE - A former special agent with the U.S. Environmental Protection Agency has been charged with obstructing justice and lying under oath in a man’s ongoing civil lawsuit over alleged malicious prosecution by the federal government.

A two-count indictment handed up this week against Keith Phillips, 61, a former special agent with the EPA’s Criminal Investigation Division in Dallas, alleges the agent lied under oath about an affair he had with an FBI special agent while the two agents and their respective agencies investigated a pollution case involving a former refinery manager in Church Point.

The FBI special agent was working out of New Orleans at the time.

The three-year investigation began in 1996 and ultimately led to indictments against Hubert Vidrine Jr. and others in December 1999 in the Shreveport-based Western District of Louisiana, which includes the Acadiana area.

Charges against Vidrine were dismissed in September 2003 after a judge ruled the prosecution’s main witness would not be allowed to testify about key aspects of the case.

Vidrine and his wife filed a civil lawsuit in federal court in Lafayette seeking $5.18 million from the federal government in July 2007.

The lawsuit alleges that despite weak evidence and an unreliable witness, the Justice Department and EPA agents opted to “continue their efforts to coerce Mr. Vidrine into a plea bargain that would result in the loss of his reputation, in exchange for saving theirs.”

The civil case went to trial in June, but a judgment has yet to be handed down.

The charges against Phillips stem from a November 2008 deposition in which Phillips was asked by Vidrine’s attorney about the relationship with the FBI special agent.

Phillips was questioned about the alleged affair in an effort to determine if he had motives that were unconnected to the evidence gathered in the criminal investigation, according to the indictment.

The indictment states Phillips offered false testimony under oath by denying the existence of the past extramarital affair, called the special agent to influence her not to disclose the affair and gave a false explanation for his false testimony to his supervisor.

During the Nov. 25, 2008, deposition, Phillips allegedly told the attorney he and the FBI special agent were “close friends,” according to the indictment.

“Did you have an affair with her?” the attorney asked.

“No. No. I take offense to you even putting that in the record,” Phillips responded. “I’ve been married 31 years and you don’t stay married 31 years by having extramarital affairs.”

The indictment alleges that between Nov. 25, 2008, and March 2011, Phillips called the special agent on more than one occasion in an attempt to influence her not to disclose the existence of their past extramarital affair, explaining to her that he had testified that their relationship was only professional and a friendship.

In March 2011, a supervisory attorney from the U.S. Attorney’s Office for the New Orleans based Eastern District of Louisiana called Phillips’ supervisor and told him about Phillips’ testimony.

The supervisor then spoke with Phillips, who admitted he had an affair but falsely told the supervisor the questions in the deposition were limited to the time frame after Phillips had became a special agent in December 1998.

The indictment was handed down Wednesday but not uploaded into PACER, which provides online access to federal court records, until Friday.

Phillips was employed by the EPA from 1991 to July 26, 2011, according to the indictment.

If convicted, Phillips faces a possible maximum 10-year prison sentence and $250,000 fine on the obstruction of justice count and a possible maximum 5-year prison sentence and $250,000 fine on the perjury count.