The Securities and Exchange Commission has an investigation that could uncover another instance of brokerage firms considering their bottom line ahead of their investors, the New York Times reported.

The SEC is looking into more than 10 brokerage firms, including Morgan Stanley, Merrill Lynch, Ameritrade, Charles Schwab and E*Trade Financial, suspecting the firms failed to get the best prices for their customers on Nasdaq-listed securities when the markets open for the day. The first minutes of the day are an intense trading period as the backlog of trade requests from the previous day's post-closing activities are processed.

Four years worth of data has shown investigators that trades often favored brokerages over their clients, the Times reported, referring to sources who have been briefed on the inquiry.

One of the industry's golden rules is to secure the best price for investors. If the investigators' hunches pan out, the fall out would add up to pennies per share for investors, but represent a lot of money for brokers.

Wall Street has been rocked in recent years by conflict of interest scandals that have favored industry insiders over regular investors.

The investigation is expected to put traders on notice that the SEC is watching to make sure “best execution” obligations are being met. At issue are two areas known as internalization and payment for order flow. Both are permitted by the S.E.C., and while they have long been controversial, as they appear to pit the interests of a brokerage firm against those of its clients, they are illegal only if the customer does not receive the best price available, the Times reported.

"Firms are obligated to seek the best possible executions for their customers' orders, irrespective of payment for order flow or other inducements," an SEC statement related to the study said. "However, payment for order flow and internalization create conflicts of interest for brokers because of the tension between the firms' interests in maximizing payment for order flow or trading profits generated from internalizing their customers' orders, and this fiduciary obligation to route their customers' orders to the best markets."