Afghanistan summoned Pakistan’s ambassador in Kabul and lodged a formal protest after cross-border shelling in eastern Kunar province killed at least eight Afghan border police on Tuesday.
The new dispute between the two neighbors comes as Afghanistan celebrates its country's 96th Independence Day.
According to local media the incident happened in Kunar's Nari district when Pakistani troops started shooting across the border on Monday after finding one of their men dead at an outpost.
The Ministry of Foreign Affairs of Afghanistan said a strong protest was lodged with Ambassador Syed Abrar Hussain over the artillery fire from Pakistan's military, adding that relations between the two countries could be marred.
"Continuation of such movements by the Pakistan military ... will have adverse effects on bilateral relations," a statement by the ministry said, adding the ambassador had promised to convey “Afghanistan’s concerns to the officials.”
Afghanistan's President Ashraf Ghani has accused Pakistan of not doing enough to crack down on Taliban militants after a series of attacks during the past week killed more than 56 people in the country, in a rare public rebuke.
People in Afghanistan have also expressed anger towards Pakistan, which is considered to have influence over the militant group.
"I've come to celebrate our Independence Day, we're celebrating against Pakistan," Kabul resident Mohammad Zamir told Reuters, near the ruins of houses and shops destroyed by a bomb earlier this month.
Wearing traditional Afghan dress, President Ashraf Ghani and others attended the celebrations for the first time since most NATO forces withdrew from the region.
The deadly attacks came just after the revelation of Taliban founder Mullah Omar's death and claims of a split in the group over the election of new Taliban chief Mullah Akhtar Mansoor.
However, Pakistan was quick to deny claims of responsibility and condemned the attacks by saying it "is committed to maintaining good neighbourly relations with Afghanistan."
Afghanistan's border with Pakistan was defined in a 1919 treaty recognising Afghan independence from the British empire, although the country was never fully colonised.
As the country celebrates its 96th anniversary of independence on on August 19, many Afghans question the presence of foreign troops.
The Taliban stated that Afghans should fight against occupation today as their forefathers did against the British Empire, Reuters reported.
Afghanistan has repeatedly accused Pakistan of turning blind eye to the Taliban despite peace talks between Islamabad and the Afghan government. Ghani has pushed for the talks to end 14 years of violence that has claimed more than 40,000 lives in the country.
Both sides said they will continue talks in the future but violence has not stopped in the war-torn country.