Saturday's decision by the office of the US Trade Representative (USTR) was widely seen as siding with Apple against the South Korean technology giant in a long-running legal dispute between the two rivals.
The move effectively vetoed a product ban imposed by the US International Trade Commission (USITC) on some iPhone and iPad models for patent infringement against Samsung.
It was the first time the USTR has overruled the commission since 1987, and South Korea's trade ministry made its feelings clear.
"Our ministry expresses concern about negative impacts the decision by the USTR will have on protecting patents held by Samsung," it said in a statement.
The ministry also said it would "closely watch" a USITC ruling expected on August 9 on whether some Samsung devices violated Apple's patent.
"We hope that the ruling by the USITC...and further decisions by the US administration will be made on fair and reasonable grounds," the statement said.
Samsung -- the world's largest technology firm by value and also the top smartphone maker -- has been locked in a series of bitter patent battles with Apple across a number of countries including Germany, Japan and the United States.
The ban overturned by the USTR covers devices that are no longer actively sold in the US market such as iPhone 3 as well as the iPad 3G and iPad 2 3G.
But it is still seen as a blow to Samsung, which said it was "disappointed" at the decision.
In a separate battle in US federal court, Samsung was ordered last August to pay more than USD 1 billion for patent infringement, a ruling which also opens the door to a ban on some Samsung devices.
A judge later slashed the award to USD 598.9 million.