NEW YORK (CNN/Money) - Merrill Lynch & Co. Friday suspended Martha Stewart's stock broker as investigators try to get to the bottom of how her trades were handled in the stock of ImClone Systems Inc., whose CEO has been charged with securities fraud.

The nation's biggest brokerage said it placed broker Peter Bacanovic, and his assistant Douglas Faneuil, on paid leave pending further investigation.

The brokerage firm said it took the action on its own after an internal investigation raised factual issues regarding a client transaction. "This information came to the attention of the company's law and compliance department during the past 48 hours," Merrill said in a statement.

Merrill's actions come as the probe into ImClone deepens. On Dec. 28, the Food and Drug Administration refused to consider ImClone's (IMCL: Research, Estimates) application for a new cancer drug, Erbitux, causing the company's stock to plunge.

Bacanovic is the broker for ImClone co-founder and former CEO Sam Waksal and his daughter Aliza, as well as Stewart. Waksal was charged last week for allegedly tipping off two family members a day before the FDA made its announcement. He has denied any wrongdoing.

"It's my understanding that Merrill Lynch uncovered some discrepancies in the statements of these two employees as they prepared to meet with our investigators next week," Ken Johnson, a spokesman for the House Energy and Commerce Subcommittee, told the Associated Press. The subcommittee is investigating the ImClone case.

"This action only confirms our suspicions that we are on the right track and getting very close to the truth," he added. Johnson said Stewart was not the focus of the investigation, "but we continue to pursue leads relating to public statements she has made."

Stewart has come under scrutiny from congressional investigators and federal prosecutors over the sale of nearly 4,000 shares of ImClone on Dec. 27, the day before the FDA's announcement regarding Erbitux.

Stewart repeatedly has denied having any insider knowledge and said she had previously arranged for Bacanovic to sell her shares if the price dipped below $60, which it did on Dec. 27. Stewart has not been charged and has turned over phone records and logs from her private jet to congressional investigators that show she tried unsuccessfully to call Waksal on the day of her trade.

CNNfn has learned that the apparent discrepancies related to the sale by Stewart and whether it was pegged to a target price. Both the U.S. Attorney for the Southern District of New York and the Securities and Exchange Commission are looking into this new information, a source familiar with the situation said.

New York-based Merrill said it is continuing to cooperate in the investigation. Calls to Stewart and Peter Bacanovic were not returned Friday.

ImClone said earlier this week that the SEC may take civil action against it.

-- Associated Press contributed to this report