The Obama administration sought to intimidate witnesses into not testifying to Congress on Tuesday about whether ATF knowingly allowed weapons, including assault rifles, to be “walked” into Mexico, the chairman of a House committee investigating the program said in an interview Monday.

House Oversight and Government Reform Committee Chairman Darrell E. Issa, California Republican, said at least two scheduled witnesses expected to be asked about a controversial weapons investigation known as “Fast and Furious”received warning letters from the Bureau of Alcohol, Tobacco, Firearms and Explosives to limit their testimony.

Mr. Issa’s committee is set to hear testimony from six current or former ATF employees, including agents and attaches assigned to the bureau’s offices in Mexico, about the operation — in which, federal agents say, they were told to stand down and watch as guns flowed from U.S. dealers in Arizona to violent criminals and drug cartels in Mexico.

The six-term lawmaker aired his concerns about the program in a wide-ranging interview with reporters and editors at The Washington Times on Monday.

Among other questions, the agents are likely to be asked about a large volume of guns showing up in Mexico that were traced back to the Fast and Furious program; whether ATF officials in that country expressed concerns about the weapons to agency officials in the U.S., only to be brushed aside; and whether ATF officials in Arizona denied ATF personnel in Mexico access to information about the operation.

Nearly 50 weapons linked to the Fast and Furious program have been recovered to date in Mexico. Committee investigators said Mexican authorities also were denied information about the operation.

Mr. Issa also said he is certain the Fast and Furious operation was known by most top officials at the Justice Department and that Attorney General Eric H. Holder Jr. either knew and misled Congress, or was so out of the loop that he’s guilty of mismanagement.

“How is it that the No. 2, 3, 4 at Justice all knew about this program, but the No. 1 didn’t?,” Mr. Issa said. “Is it because he said ‘don’t tell me’? Is it because they knew what they were doing is wrong, and they were protecting their boss? Or is it that Eric Holder is just so disconnected … ?

“Whichever it is — he knew and he’s lied to Congress, or he didn’t know, and he’s so detached that he wasn’t doing his job — that really probably is for the administration to make a decision on, sooner not later,” Mr. Issa said.

Those scheduled to testify are William McMahon, ATF deputy assistant director for field operations in Phoenix and Mexico; William Newell, former ATF special agent in charge at the Phoenix field division; Carlos Canino, ATF acting attache to Mexico; Darren Gil, former ATF attache to Mexico; Jose Wall, ATF senior agent in Tijuana, Mexico; and Lorren Leadmon, ATF intelligence operations specialist.

But after receiving subpoenas, at least two of the agents got letters from ATF Associate Chief Counsel Barry S. Orlow warning them to keep certain areas off-limits, including those still under investigation. Neither of the targeted agents was identified.

Mr. Issa said at least one witness wanted to back out of testifying to his committee after receiving the letter, but the chairman declined that request. Instead he fired a letter back to William J. Hoover, deputy director of ATF, saying the “timing and content of this letter strongly suggest that ATF is obstructing and interfering with the congressional investigation.”

ATF, in a statement, said letters sent to agents subpoenaed to testify before Congress are “essentially the same as the standard document provided to ATF witnesses subpoenaed to testify in court.” It said the witnesses are “encouraged to answer fully and candidly all questions concerning matters within his personal knowledge,” but provide “guidance” about revealing statutorily prohibited information.

Mr. Orlow did not return messages left on his office and cell phones.