The probe, called “Operation Choke Point,” was revealed in documents released by the House Oversight Committee on Thursday, and further detailed in a news report by Reuters.

The DOJ had been investigating four payment processors, a bank and officials as part of criminal cases starting in November 2013, according to Reuters. Meanwhile, 10 other banks and payment processors have been investigated for civil fraud.

But House Republicans raised questions about the investigation for unfairly tarnishing the reputation of the banks in the prosecutors’ crosshairs. U.S. Rep. Darrell Issa, the oversight panel leader, called the probe an “abuse of power.” He added, “if the administration believes some businesses should be out of business, they should prosecute them before a judge and jury.”

The House committee said the DOJ’s investigation denies merchants the ability to survive by cutting off access to funding. “Operation Choke Point has forced banks to terminate relationships with a wide variety of entirely lawful and legitimate merchants,” it said.

The DOJ, however, insists that investigations only take place when firms break federal laws. In an email to Reuters, a DOJ spokeswoman, wrote, “when financial institutions choose to process transactions, even though they know the transactions are fraudulent or are willfully ignorant of that fact, they are breaking federal law and we will not hesitate to hold them accountable.”

Separately, the Securities and Exchange Commission is looking into whether Charles Schwab (SCHW) and Bank of America’s Merrill Lynch unit (BAC) failed to do enough to stop illegal activity by some of their clients. In a few cases, drug dealers allegedly opened accounts at the institutions to launder their proceeds.