NEW YORK (CNN/Money) - Merrill Lynch CEO David Komansky apologized Friday for recent e-mails that have come to light from the brokerage house's analysts that he said had compromised the integrity of the firm's research department.

Komansky said the e-mails released by New York Attorney General Eliot Spitzer "fall far short of our professional standards" and the company regrets that the perception of its research integrity has been questioned.

The e-mails, including some from former analyst and Internet guru Henry Blodget, suggest Merrill (MER: up $0.46 to $42.96, Research, Estimates) analysts were uncomfortable with the pressure being applied by investment banking customers in reaction to potential negative comments from analysts.

"We have failed to live up to the high standards that are our tradition, and I want to take this opportunity to publicly apologize to our clients, our shareholders and our employees," Komansky said.

Komansky's apology comes a day after Securities and Exchange Commission Chairman Harvey Pitt announced a formal investigation of analysts' conflicts of interest.

"This is the next step -- and a critical one -- in the Commission's year-long review of analyst practices," Pitt said in a statement.

"The recent disclosures that resulted from the investigation by the New York state attorney general, as well as the practices uncovered by the staff of the SEC, the NYSE and NASD, reinforced the commission's conclusion that further inquiry is warranted," Pitt said.

Komansky said Merrill will help the SEC and NASD develop new research rules that will apply to all brokerage houses.

"We applaud the company," Spitzer's office said "Recognizing and understanding the problem is a critical first step. We are hopeful of resolving the matter shortly with Merrill Lynch."

Last week Merrill agreed to Spitzer's demand for disclosure on a Web site of the firm's banking relationships with companies it covers and in its research reports. Spitzer and Merrill continue to discuss further terms of a possible settlement, including a monetary fine.

Komansky said that as the brokerage firm continues discussions with Spitzer, it will adopt new policies to restore investor confidence in its research arm.

"We will take meaningful and significant actions to restore investor confidence," he said. "We will redouble our enforcement of existing policies and take strong actions against anyone who violates them."

The e-mails released by Spitzer April 8 led to a court order for Merrill to institute immediate reforms to its research department.

"The more I read of these, the less willing I am to cut companies any slack, regardless of the predictable temper-tantrums, threats and/or relationship damage that are likely to follow," reads one e-mail from well-known Internet analyst Henry Blodget. "If there is no new e-mail forthcoming from [Merrill management] on how the instructions should be applied to sensitive banking clients/situations, we are going to just start calling the stocks ... like we see them, no matter what the ancillary business consequences are."

Merrill initially said the e-mails showed no evidence of wrongdoing.