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A week after two Republican lawmakers raised concerns over what they saw as a threatening video from the new head of the Alcohol, Tobacco, Firearms and Explosives bureau, Acting Director B. Todd Jones has issued a "special message" to all ATF employees clarifying his remarks in the video.

The message, sent in written form through an internal system, notes that ATF policy telling employees to raise concerns "through the chain of command" can be trumped by an employee's right to become a protected whistle-blower. And in a letter Wednesday to the lawmakers, Jones insisted that "at no time" was he "attempting to discourage, dissuade or prevent employees from" becoming whistle-blowers.

"This latest video message ... was designed to reinforce and highlight the importance of accountability at all levels of ATF to (promote) safe and efficient Federal law enforcement, one of the main concerns raised to me by employees in the field," Jones wrote in the letter, obtained by Fox News.

Nearly three weeks earlier, he distributed a video message to ATF personnel titled "Choices and Consequences."

"Choices and consequences means simply that if you make poor choices, that if you don't abide by the rules, that if you don't respect the chain of command, if you don't find the appropriate way to raise your concerns to your leadership, there will be consequences, because we cannot tolerate -- we cannot tolerate -- an undisciplined organization," Jones said in the video.

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It was the eighth video from him, distributed throughout an agency still reeling from the scandal over Operation Fast and Furious. The botched gun-running probe, led by ATF and federal prosecutors in Phoenix, was brought to light by whistle-blowers within ATF's ranks.

After at least one unidentified ATF employee sent the "Choices and Consequences" video to Rep. Darrell Issa, R-Calif, and Sen. Charles Grassley, R-Iowa, who are leading a congressional investigation into Fast and Furious, the pair fired off a letter to Jones.

They said his "ominous" message "could be interpreted as a threat" and is "likely to have a major chilling effect on ATF employees exercising their rights to contact Congress." And they wanted Jones to explain his video.

Issa went further days later on Fox News, saying, "I don't think (the public) can reach any other conclusion except this is a thinly veiled threat, telling people, 'Don't go to the press, don't go to Congress, even if the chain of command isn't working,'" He said the video would "lead to whistle-blowers not doing the right thing."

In his letter Wednesday, Jones told the lawmakers he uses "brief internal video messages ... as a means to communicate efficiently with our nearly 5,000 employees throughout the country and in our international posts of duty." Past topics have included "Trust," "Morale," "Mission," "Change," "ATF's Role in the Department of Justice," "Leadership and Organizational Discipline," he wrote.

The video series is intended "to strengthen and improve ATF," Jones told ATF employees in the internal message Wednesday, obtained by Fox News. The "Choices and Consequences" video specifically "focused on the need for accountability at all levels of ATF -- from senior management to the most junior employees," he said.

"One of the main employee concerns expressed to me since my appointment has been the lack of accountability for those who do not abide by the rules ... (and the video) specifically addressed employee concerns about accountability," Jones wrote. "(The video) was not intended in any way to discourage disclosures covered by the Whistleblower Protection Act or imply that employees would be disciplined for making such protected disclosures."

At least one of the initial Fast and Furious whistle-blowers said the original concerns about Jones' video were "off base," though he praised Grassley and Issa for "following up on concerns that are being relayed to them."

"I didn't see (the video) as threatening, especially when taken into context with the previous videos that were put out," said Peter Forcelli, who helped blow the whistle on Fast and Furious from his time in Phoenix. He said he was "surprised" that ATF colleagues would raise concerns about the video, and he told Issa's and Grassley's offices as much.

In an interview with Fox News, Forcelli said ATF has had "problems" with whistle-blower cases in the past, and he believes Jones' "Choices and Consequences" video was trying to "dissuade people from putting stuff on message boards and on the blogs."

"Unfortunately some of the things that have been discovered at ATF haven't been reported to the chain of command," Forcelli said. "They've wound up on the Internet. It's demoralizing to the agency, and it's not good government. We need to be aware of problems in the agency from within the agency."

Both Forcelli and Larry Alt, another initial whistle-blower over Fast and Furious, praised the current leadership at ATF. Forcelli said Jones, Deputy Director Thomas Branden and other top officials are the right ones to "bring our agency back into being effective and efficient," and Alt said, "We're headed in the right direction."

Fast and Furious was launched in late 2009 by ATF officials in Phoenix, with help from federal prosecutors there. The goal was to take down an entire gun-smuggling organization. Over several months, the operation's targets bought nearly 2,000 weapons. But for reasons that are still in dispute, most of those firearms were never followed, and high-powered weapons tied to the suspects ended up at crime scenes in Mexico and the United States, including the death of Border Patrol agent Brian Terry in December 2010.

Fox News' John Brandt and Chad Pergram contributed to this report.