By Rachel Louise Ensign 

A U.S. regulator fined a former MoneyGram International Inc. chief compliance officer Thursday, in a rare case of a compliance staffer being held responsible for controls failures.

The Treasury Department's Financial Crimes Enforcement Network handed down a civil penalty of $1 million on the former executive, Thomas Haider, for allegedly not ensuring that his former employer followed anti-money-laundering laws. The fine raises the stakes for compliance officers, who have grown increasingly concerned about being held liable for on-the-job decisions.

FinCEN, which is responsible for enforcing money-laundering laws and collecting data on potential financial crimes, is also seeking to bar him from the financial industry. The Manhattan U.S. attorney's office on Thursday sued Mr. Haider in an effort to collect the penalty and enforce the ban.

Mr. Haider believes the allegations are "unfounded," his attorney Ian Comisky of Blank Rome LLP said in a news release.

Top compliance staffers at global companies have rarely faced such penalties, and the penalty is a sign that FinCEN is following through on its promises to increasingly hold individuals responsible for lapses in corporate controls. Other regulators are vowing to take the same approach.

"I think this makes good on our commitment that we've made from the time I came to FinCEN that we will at least consider individuals in every investigation we pursue," director Jennifer Shasky Calvery said in an interview.

The agency has raised its profile under the leadership of Ms. Shasky, a former prosecutor who took on her role in 2012. Since then, FinCEN has said it would focus on individuals as well as previously overlooked areas of enforcement such as casinos and money-services businesses.

"While the current government mantra is for heightened individual responsibility, this is the wrong case to try to establish this principle," Mr. Comisky said.

Compliance staffers have become a hot commodity in recent years as financial-services firms have tried to bolster controls in the wake of huge fines and new regulatory scrutiny. Some have gone so far as to say these employees may choose another line of work if they fear being fined.

News of the agency's probe of Mr. Haider as well as the penalty of another high-profile compliance staffer have stirred fears among compliance workers. Some now say they worry that they could be penalized for decisions they make in the course of their work.

"Many of my colleagues are absolutely terrified," said Bob Werner, global head of financial crime compliance at HSBC Holdings PLC and a former head of FinCEN, speaking at a conference in September.

Mr. Haider's attorney, Mr. Comisky, also raised this concern on Thursday. "This lawsuit is unprecedented and will undoubtedly have a chilling impact on those who work, or seek to work, as compliance officers at U.S. financial institutions," he said.

But Ms. Shasky said that most compliance officers have nothing to fear. "We consider compliance officers to be our most valued partners. We recognize that the vast, vast majority are out there doing the right thing every day," she said. "That being said, there are times, unfortunately, where people don't live up to their responsibilities."

Mr. Haider was chief compliance officer at the money-transfer firm from 2003 to 2008, the U.S. attorney's office said. The former executive can now fight the penalty in court.

FinCEN alleges that Mr. Haider didn't file suspicious-activity reports, which financial institutions are required to file under anti-money-laundering laws, on agents "whom he knew or had reason to suspect were engaged in fraud, money laundering, or other criminal activity," the release said.

He also allegedly didn't take action against agents based on complaints he received, which "led to thousands of innocent individuals being duped out of millions of dollars," the release said.

The probe of Mr. Haider is connected to the investigation of MoneyGram that the company settled with the U.S. Department of Justice in 2012 for $100 million, two people familiar with the matter said. As a part of the settlement, the firm admitted criminally aiding and abetting wire fraud and failing to maintain an effective anti-money-laundering program in connection with a fraud scheme between 2004 and 2009.

"Tom Haider has not been an employee of MoneyGram since May 2008. Since that time, MoneyGram's management, organizational structure, and programs have changed significantly. It is MoneyGram's policy not to comment on ongoing litigation," a MoneyGram spokeswoman said in a statement.

The fine comes just months after another regulator penalized a high-profile compliance officer, a move that stirred alarm in the profession.

In February, the Financial Industry Regulatory Authority fined Harold Crawford, Brown Brothers Harriman's global anti-money-laundering compliance officer until the end of last year. Finra alleged that Brown Brothers and Mr. Crawford failed to establish an anti-money-laundering program that could reasonably detect and report potentially suspicious activity, a task that is generally the goal of such a program.

Brown Brothers Harriman agreed to pay a record $8 million fine. Mr. Crawford was fined $25,000 and suspended for one month. Neither the firm nor Mr. Crawford admitted or denied guilt as part of the settlements. Mr. Crawford moved to a job at an affiliate of the firm, according to the Finra action.

That penalty led even those at the very top of the compliance profession to become concerned about individual liability.

After hearing about Finra's penalty of Mr. Crawford, Bill Fox, head of global financial crimes compliance at Bank of America Corp. asked bank leaders "'what are we doing about liability insurance?'" according to a video recording of remarks at a March conference. "I never ever thought I would have that conversation." Mr. Fox, himself also a former head of FinCEN, also said he knew and respected Mr. Crawford "a great deal."

Write to Rachel Louise Ensign at rachel.ensign@wsj.com

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