"We believe that these 43 cases deserve special attention from the Army due to the nature of their allegations," the letter said, according to a copy posted on the website for Sen. Richard Blumenthal, D-Conn.
For the broadcast report, the Pentagon had arranged for ABC News to interview Lt. Gen. William Phillips of Army acquisition about the concerns, but later canceled, his staff saying "they will be declining an interview for some time in the foreseeable future."
When ABC News appeared at the Pentagon office that handles the debarment of contracts, the officer in charge said he was not allowed to answer questions without permission.
"Well, there are certain regulations that have to be followed, due process regulations," he began, presumably referring to the contract debarment process. "That gets into things that I cannot discuss. In fact, I'm not allowed to talk to you unless I have the permission of the Army so I'll have to end this interview at this time."
In a previous statement to ABC News, the Army said it has "extensive vendor vetting procedures to prevent the awarding of contracts to such vendors." It said most of the 43 companies were not awarded any new contracts "as a result of measures currently in place."
"The army takes seriously any allegations of improper contractor activities and has vigorous processes to ensure that those with whom we do business are not supporting the insurgency or otherwise opposing U.S. and collation forces in Afghanistan" the statement said.
Sopko's newly released alert letter calls into question those assurances. The Pentagon did not immediately respond to a request for comment about the letter.
Inspector General Sopko says the Army needs to permanently block the companies from receiving any more U.S. taxpayer money, given the seriousness of the information.
"I am a former prosecutor, I've seen the information and it made my hair stand on end," Sopko told ABC News.
Representatives for the two companies referenced in this report separately told ABC News the companies denied any ties to terrorism and were contesting their inclusion on the SIGAR's list.
While the evidence against all the companies remains classified, the SIGAR told ABC News it is very specific and overwhelming.