Following the New York Attorney General’s investigation of Merrill Lynch’s research practices, the firm was fined $100 million in what company president Stanley O’Neal called “a political event.”

The attorney general’s office is in the midst of an ongoing investigation of other firms, including Morgan Stanley, which is fighting back.

According to sources, Morgan Stanley has told the NASD and the attorney general’s investigating unit that it “opposes” a fine similar to Merrill’s, claiming it has done “nothing wrong.”

“Why should we pay a fine, essentially admitting guilt, when we know we’re clean,” says a source.

The $100 million fine that Merrill was hit with was in part the result of the attorney general’s office uncovering e-mails that revealed that stock analysts gave favorable ratings to companies to win investment-banking business.

But according to sources, attorney general Eliot Spitzer has so far “not found” any Morgan Stanley e-mails that suggest its analysts gave tainted ratings in order to win investment banking clients.

Morgan Stanley, meanwhile, is also against splitting research from banking, claiming “it would harm the capital-raising process,” a source says.

The SEC, NASD and the NYSE have been in discussions with several Wall Street firms to settle conflict of interest investigations. The parties have talked about fines and reducing conflicts by altering the relationship between research and investment banking units.

But Morgan Stanley has told regulators that analysts help bankers identify “promising” companies for IPOs, and reject IPOs that would make poor investments for the firm’s clients, according to a source.