The Securities and Exchange Commission Tuesday brought charges against a credit rating firm that prides itself on its independence, citing the Egan-Jones Ratings Company and its owner and president Sean Egan for “material misrepresentations and omissions” in a 2008 application.

The charges center around statements made when Egan-Jones applied in 2008 to become a Nationally Recognized Statistical Rating Organization (NRSRO) in asset-backed securities and government securities.

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Also named was president Sean Egan, who told CNBC in advantage of the filing that his firm had fought with the SEC for 15 years on various matters and "we won't be intimidated by anybody."

EJR and Egan also were charged with material misrepresentations in other submissions and violations of record-keeping and conflict-of-interest provisions governing NRSROs.

The SEC’s Division of Enforcement in seeking hearings and a cease-and-desist order said that EJR in its 2008 application falsely stated that it had 150 outstanding ABS issuer ratings and 50 outstanding government issuer ratings.

The SEC also said:

“EJR further falsely stated in its 2008 application that it had been issuing credit ratings in the ABS and government categories as a credit rating agency on a continuous basis since 1995. In fact, at the time of its July 2008 application, EJR had not issued — that is, made available on the Internet or through another readily accessible means — any ABS or government issuer ratings, and therefore did not meet the requirements for registration as an NRSRO in these categories. EJR continued to make material misrepresentations regarding its experience rating asset-backed and government securities in subsequent annual certifications furnished to the SEC.”

Jones, in discussing the case with CNBC, noted that the SEC charges were about paper work and filings, not there has “never been any question about ratings.”

Egan-Jones prides itself on taking no compensation of any type from the issuers of debt or other securities and providing unbiased ratings, as a result.

It says on its web site:

Our unbiased, rules-based methodology and corporate credit ratings with zero issuer influence on approximately 1,000 very widely held IG, Crossover and HY corporations assist clients minimize portfolio risk and exploit unrecognized opportunity.

And Jones told CNBC that all the statements in the firm’s filings have been honest and truthful.

Lawyers for Egan-Jones have previously said they plan to contest the SEC's lawsuit, Reuters reported.

The SEC also alleges that EJR made other misstatements and omissions in submissions to the SEC by providing inaccurate certifications from clients, failing to disclose that two employees had signed a code of ethics different than the one EJR disclosed, and inaccurately stating that EJR did not know if subscribers were long or short a particular security.

In 2008, Egan appeared before Congress on October 22, 2008 and argued that issuers of complex securities "shopped" for ratings which resulted in a race to the bottom in terms of credit transparency.