"Any decision by the US to declare the Haqqani network a terror group will not be a good sign for future Pakistan-US relations,” the official told Agence France Presse.
Secretary of State Hillary Clinton's announcement came less than a month after Congress passed the resolution calling upon the State Department to put the Pakistani-based terror group on the State Department's list.
Officially, Islamabad remained noncommittal over Clinton's decision on Friday to name the Haqqani group an official terrorist organization.
"It is not our business," Pakistan embassy spokesman Nadeem Hotiana said in a statement, adding the country's government remained committed to "combating extremism and terrorism" in the region.
However, the group is reportedly one of many Islamic extremist organizations in the region receiving support from Pakistan's Inter-Services Intelligence directorate, also known as ISI.
Former Chairman of the Joint Chiefs of Staff Adm. Mike Mullen accused the Haqqani Network of being a "veritable arm" of ISI.
In the past, ISI agents helped support and equip members of the Taliban as they swept into Afghanistan after the Soviet Union's withdrawal in the late 1980s.
Pakistan's intelligence agency has also been accused of providing security for top Taliban leaders, including Mullah Omar, who are seeking refuge inside the country.
That said, the Pakistani official noted that "saner elements within the US administration" understand the detrimental impact the decision to add the Haqqani group to the terror list will have on American ties to Islamabad.
However, DOD spokesman George Little had nothing but praise for the decision.
"These new group designations will build on our efforts to degrade the Network's capacity to carry out attacks, including affecting fundraising abilities, targeting them with our military and intelligence resources, and pressing Pakistan to take action," Little said in a statement released Friday.
American commanders in Afghanistan have accused the Haqqani Network of carrying out deadly cross-border attacks that have produced some of the heaviest fighting since the Obama administration surged more than 20,000 U.S. troops into the southern part of the country in 2009.
Most recently, Haqqani gunmen engaged in a brutal firefight with Afghan National Security Forces at a hotel outside of Kabul in June. Nearly 20 Afghan civilians were killed and more wounded during the 12-hour standoff, according to news reports at the time.
That said, U.S.-Pakistani tensions had started to ease in July when Islamabad decided to re-open key supply lines into Afghanistan to U.S. and coalition forces.
As part of that deal, Clinton issued a rare apology for the errant air raid by U.S. and NATO warplanes that killed 24 Pakistani soldiers last November.
While the White House and the Pentagon have repeatedly expressed their regret for the air raid, no one from the Obama administration had formally or informally apologized for the attack until Clinton.
—Jeremy Herb contributed to this report