Design flaws in a $6.9 million crossing under construction on the Afghan-Pakistan border may pose a security risk, a government watchdog warned Thursday.

Almost half of Afghanistan's annual national budget came from customs revenues in 2012, according to Special Inspector General for Afghan Reconstruction John F. Sopko, which means secure borders are important to the country's financial well-being as well as its security.

Sopko said in an IG alert letter to U.S. military officials that he believes design problems will slow traffic at the Weesh-Chaman crossing in Kandahar Province.

The Weesh crossing has only one entry control point, which Sopko said is contrary to military guidance. The single entry point will also have an inspection device in one lane, leading to backed-up traffic, which can become a security risk.

"Increased congestion directly affects inspection efficiency and security within the border crossing point," Sopko wrote in the letter, addressed to officials at the U.S. Army Corps of Engineers, NATO in Afghanistan, the Combined Security Transition Command-Afghanistan and the International Security Assistance Force regional command.

The IG sent the warning letter on Oct. 3, intending to release the letter publicly on Thursday. But on Wednesday, U.S. Forces Afghanistan made public its response discounting SIGAR's concerns.

"USFOR-A recognizes SIGAR’s concerns, but believes that the standards used by SIGAR are not applicable in this case," the letter said.

USFOR-A, part of the International Security Assistance Force, argued the single entry control point is common practice because it provides the most control over cargo coming into the country and doesn't slow traffic as much as SIGAR worried.

The guidance calling for two entry points refers to facilities with long-term housing, not border control points, USFOR-A said. And the benefits of the inspection device will outweigh the slight traffic impact, the letter said.

Sopko "strongly disagreed" and said USFOR-A misinterpreted the design guidance.

"This view is not shared by officials from either the U.S. Army Corps of Engineers or NATO Regional Command-South, both of whom voiced serious concerns over installation of the device," Sopko said. "In fact, Regional Command-South issued a formal letter of nonconcurrence related to the device’s installation."

Read the alert letter here.