The Financial Industry Regulatory Authority has censured and fined Piper ­Jaffray & Co. $700,000 for failing to retain about 4.3 million e-mails over a six-year period and for not alerting FINRA that it was having problems with its e-mail retention and retrieval.

FINRA announced the action yesterday, stating in an enforcement document that it stemmed from an investigation of an employee whose e-mails did not include one dated Dec. 7, 2004, that the authority’s investigators already had in paper form. After further inquiry, FINRA found the e-mail problems existed throughout the firm from November 2002 through December 2008.

This is the second enforcement action against the Minneapolis-based firm for the failure to retain e-mails.

The Securities and Exchange Commission, New York Stock Exchange and NASD — now FINRA — censured and fined Piper Jaffray $1.65 million in November 2002 for e-mail problems and directed the firm to certify that it had systems in place to comply with the rules.

The enforcement document associated with the most recent case shows that, after the initial sanctions, Piper failed to establish a supervisory system and procedures designed to detect and remedy deficiencies in its e-mail systems or ensure compliance with recordkeeping and reporting requirements.

“E-mail retention is a critical regulatory requirement with which broker-dealers must comply,” James S. Shorris, FINRA executive vice president and acting enforcement director, said yesterday. “Piper Jaffray failed to disclose that it was not making complete production of its e-mails due to intermittent problems with its systems — potentially preventing production of crucial evidence of improper conduct by the firm and its employees.”

But the firm responded to the enforcement action by stating its e-mail retention problems were “inadvertent,” “isolated” and “caused by technology issues.”

Piper Jaffray said “over the entire period reviewed we retained approximately 98% of e-mails rather than 100% as we were required to do. The overwhelming majority of these issues occurred prior to Aug. 1, 2006.”

The firm said it “has taken multiple steps to improve its archival capabilities over time” and that its e-mail retention has improved to effectively 100%.”