After a freight train carrying toxic chemicals derailed in East Palestine, Ohio, in February, Transportation Secretary Pete Buttigieg secured what seemed like a significant victory. Following years of resistance, the nation’s largest freight railroads agreed to participate in a federal safety program that allows employees to confidentially report safety issues.

But five months after that commitment, none of the railroads have formally joined the program. Though they say they still intend to participate, the companies have raised concerns about the initiative, saying it is flawed and needs to be overhauled, according to government and industry officials.

The railroads’ hesitation raises questions about whether a key step to improve rail safety that Mr. Buttigieg hailed in the wake of the East Palestine derailment will come to pass. And it illustrates the steep challenge looming over federal officials and lawmakers as they push for safety changes after the Ohio accident, sometimes against the wishes of the freight rail industry. In Congress, a rail safety bill with bipartisan support faces an uncertain fate.

“Too often, after a major rail incident, an immediate public call for better safety practices has eventually given way to industry pushback and inaction,” Mr. Buttigieg said in a statement. “That must not happen this time.”

Noting that the railroads had committed in March to joining the safety program, he added, “It is past time for them to keep their promise.”

Mr. Buttigieg extracted that commitment from an industry with a long history of flexing its lobbying muscle and fighting regulatory efforts it views as onerous. When the railroads agreed to join the program, they had come under an intense public spotlight in the wake of the East Palestine derailment.

But that scrutiny is fading, and Mr. Buttigieg’s goal of bolstering safety could be undermined if the companies secure changes to the program that end up watering it down.

The program, known as the Confidential Close Call Reporting System, began as a pilot in 2007 and was later expanded. It is voluntary for railroads, and it allows their employees to report so-called close calls — such as a train exceeding the maximum speed or a mishap with a track switch — without the fear of discipline.

The program is modeled after a Federal Aviation Administration program that allows pilots and other aviation personnel to report safety issues. Both the F.A.A. and rail programs rely on NASA to act as an independent third party that processes submissions. But participation in the rail program has been limited, with only 27 of the nation’s roughly 800 railroads currently taking part. Amtrak is part of the program, but none of the largest freight railroads participate.

In the aftermath of the East Palestine derailment, Mr. Buttigieg called on the freight rail industry to take a number of steps to improve safety. One of his requests was that the major railroads join the confidential reporting program, saying it had a proven track record of reducing accidents and keeping workers safe.

“By refusing to take this common-sense step, you are sending an undesirable message about your level of commitment to the safety of your workers and the American communities where you operate,” Mr. Buttigieg wrote to the chief executives of the major freight railroads in late February.

In a letter to Mr. Buttigieg a few days later, Ian Jefferies, the president and chief executive of the Association of American Railroads, a trade group, said that all of the largest freight rail companies had agreed to join the program. But he noted that they had similar internal programs, and he cited several aspects of the federal program that could be improved.

For instance, Mr. Jefferies wrote that reports submitted through the program often contained insufficient detail and were not provided to railroads in a timely fashion. He also raised the issue of employee discipline.

“In the rare situation in which an employee is misusing the system to prevent his or her unsafe decisions or actions from being addressed by the railroad,” he wrote, “the program should permit the railroad to address that repeated misconduct with the employee.”

Since Mr. Jefferies sent his letter, his organization and the freight railroads have been working with the Federal Railroad Administration, which is part of the Transportation Department, to reach an agreement on the terms of the railroads’ participation in the program.

Before the East Palestine derailment, a federal panel called the Railroad Safety Advisory Committee, which provides recommendations on safety regulations, had established a working group to look at how to expand participation in the confidential reporting program.

The potential addition of the major freight railroads to the program has been the subject of discussions at meetings of the working group in recent months. One idea under consideration is for the companies to participate in a pilot program, but a consensus on how to move forward has yet to be reached, according to government and industry officials.

Vincent G. Verna, a vice president of the Brotherhood of Locomotive Engineers and Trainmen and a member of the working group, said that although the freight rail companies continued to express interest in being part of the program, there were still disagreements over key issues, including protecting workers from discipline.

The freight railroads “do not want to relinquish their ability to discipline their employees who report something if they think there’s a rule that has been violated,” Mr. Verna said. “They want to be able to retain the ability to discipline.”

Mr. Verna said that from the perspective of workers, maintaining anonymity is critical for the program’s success. If railroad employees have reason to fear punishment for reporting safety violations, they will not use the program, he said.

The Association of American Railroads contends that the freight rail companies’ existing programs for employees to report safety issues are more effective and efficient than the federal program. The trade group also argues that workers could abuse the federal program by reporting incidents that are already known to their railroads to insulate themselves from punishment.

“You risk creating a paradigm that weakens the importance of following policies and procedures,” said Jessica Kahanek, a spokeswoman for the group.

In a statement, Warren Flatau, a spokesman for the Federal Railroad Administration, said that participating in the program was “a common-sense action to advance safety.” Referring to the major freight railroads, he added that the agency “has and will continue to engage in good-faith discussions with each Class I railroad to secure their participation in this safety program.”

Norfolk Southern, the operator of the train that derailed in East Palestine, met with the Federal Railroad Administration in May to learn about the program and expects to have further discussions this month, said Connor Spielmaker, a spokesman for the railroad.

“We are making good progress toward operationalizing our membership in the program,” Mr. Spielmaker said.

Jim Mathews, the president and chief executive of the Rail Passengers Association and another member of the working group, said that for the confidential reporting program to be effective, the freight railroads have to be willing to embrace a nonpunitive approach.

“The position that the freight railroads have taken is both unfortunate and unwise,” Mr. Mathews said. “If they truly want a safer system, then punishment and discipline cannot be the only tool in your toolbox.”