Morgan Stanley agreed Wednesday to pay $15 million to settle civil charges by the Securities and Exchange Commission that it failed to produce tens of thousands of E-mails dating back to December 2000.

The commission had sought the documents in connection with its investigations into initial public offerings and into how research analysts were compensated.

The SEC alleged that the investment bank “did not diligently search for backup tapes containing responsive E-mails until 2005”; that it overwrote backup tapes; and that it made a number of misstatements regarding the status and completeness of its productions, the unavailability of certain documents, and its efforts to preserve requested E-mails.

Morgan Stanley agreed to settle the matter without admitting or denying the allegations. Of the $15 million, $5 million will be paid to the NASD and the New York Stock Exchange in related proceedings. The investment bank also has agreed to adopt and implement policies, procedures, and training focused on the preservation and production of E-mail communications and hire an independent consultant to review these reforms.

The settlement is subject to court approval.

“The laws requiring broker-dealers to provide documents to the commission are essential to the commission’s ability to enforce the federal securities laws and protect investors,” said Linda Chatman Thomsen, director of the Enforcement Division, in a statement. “Today’s action underscores the commission’s resolve to ensure the integrity of its investigative processes.”