In a statement, the ministry said "no evidence was found to substantiate the claim," Khaama Press reported.
Pakistan's Foreign Office claimed Thursday 23 members of its Frontier Corps were murdered inside Afghanistan.
The Afghan ministry added the country's border police were "fully committed to fight against international terrorism and they have proven in the past that their sacrifices are not only for the security of Afghanistan but also for the security of the region and the world."
Afghan police would resume their investigation if Pakistan "provides any evidence in regards to this incident," the ministry said.
On Thursday, the Afghan Foreign Ministry expressed skepticism about Pakistan's claim, which it said could not be confirmed.
Alluding to Pakistan's reputation for harboring terrorist groups, the ministry said, "While we will investigate the matter thoroughly, it is our belief that any terrorist act in our region is the outcome of the short-sighted policy of using extremism and terrorism as a means of strategic influence and pursuing misperceived national interest. It is impossible to nurture venomous snakes on one's soil and wishfully think that they will only bite others."