The lawmakers said in a letter to Agriculture Secretary Ed Schafer that the incident continued a "troubling pattern of obstructing congressional efforts to understand and remedy decades of discrimination against African-American farmers."
Keith Williams, an Agriculture spokesman, said the department had not yet seen the letter, which was dated February 29.
"We would have appreciated the courtesy of receiving a letter before it went to The Associated Press," he said.
On February 27, Agriculture officials ordered auditors from the Government Accountability Office to leave its offices and told employees not to speak with them. The GAO is the nonpartisan investigative arm of Congress.
The auditors were seeking information for a review now under way of Agriculture's civil rights office, including whether the department had provided misleadingly rosy information about the office's progress in clearing discrimination complaints.
J. Michael Kelly, Agriculture's deputy general counsel, said the investigators called the department February 27 morning to say they were on their way over. He said the auditors refused to provide information about what they were investigating or let department attorneys sit in on interviews with employees.
He said the department has been cooperating with the audit for a year but will not let its employees discuss the matter until it gets more information.
Along with Obama, the letter was also signed by Reps. John Conyers, chairman of the House Judiciary Committee; Bennie Thompson, chairman of the House Homeland Security Committee; Artur Davis; Bobby Scott; and G.K. Butterfield. All are Democrats.
Many of them have been involved recently in an effort to reopen a landmark settlement that the Agriculture Department reached in 1999 with black farmers who alleged the department had routinely denied them loans and other assistance because of their race. Thousands of farmers won claims, but more than 70,000 claims were never heard because farmers missed deadlines for filing.
"For too long the USDA has failed to address complaints of discrimination seriously and protect the civil rights of America's black farmers," the lawmakers wrote. "Instructing USDA employees not to cooperate with congressional auditors is counterproductive and entirely unacceptable. ... It seems clear that the Department is trying to undermine Congress' efforts to repair decades of discrimination."