This comes after Khan told a public gathering on Friday that peace was "around the corner" in Afghanistan and a "good government will be established".
Kabul has taken a strong stance against remarks made by Pakistani Prime Minister Imran Khan who had on Monday had called for an interim administration in Afghanistan.
Afghanistan has dismissed the remarks by Khan, calling them irresponsible and interference in the internal affairs of the country.
"The Ministry of Foreign Affairs of Afghanistan summoned the counsellor of the Embassy of the Islamic Republic of Pakistan in Kabul over the recent remarks by Pakistan's Prime Minister Mr Imran Khan," Sebghat Ahmadi, the spokesperson of the ministry, said in a Tweet.
1/3 Ministry of Foreign Affairs of the Islamic Republic of Afghanistan, summoned the Deputy Ambassador of the Islamic Republic of Pakistan with respect to the recent irresponsible remarks of Pakistan's Prime Minister Imran Khan. pic.twitter.com/HnVaB5zVD2
Summoning the deputy Pak envoy in Kabul, the Afghan Foreign Ministry expressed its "grave objection" on Pakistani PM's "reckless statements" about the peace process & establishment of an interim government, "deemed such statements an obvious example of Pakistan's interventional policy and disrespect to the national sovereignty and determination of the people of Afghanistan."
The Afghanistan foreign ministry has also recalled its envoy from Islamabad for consultations in the backdrop of the comments.
Pakistan PM Imran Khan told a public gathering on Friday that peace was "around the corner" in Afghanistan and a "good government will be established".
"Negotiations have been initiated with the Taliban. God willing, our brothers in Afghanistan would live together in peace in the coming days...A good government will be established in Afghanistan, a government where all Afghans will be represented. The war will end and peace will be established there," the Pakistan Prime Minister said.
This is the second summoning of a Pakistani diplomat in 10 days by Afghan foreign ministry. Afghanistan had summoned a Pakistani diplomat on 16th March following comments by Pakistani Prime Minister Imran Khan calling for "new government in Kabul"
Afghanistan in February complained to the United Nations security council (UNSC) against Islamabad due to its engagement with the Taliban and attempts to subvert the Afghan peace process.
Pakistan government in February had invited the Taliban for talks along with the United States in Islamabad infuriating Afghanistan. The meet was cancelled by the Taliban after the letter by Afghan govt to UNSC.
Islamabad sees Afghanistan has its own backyard and since the Afghan war in the 1980s has been trying to prop up regimes, including the Taliban in 1990s, that have been hindering the development of the country.
The development comes even as pressure mounts on Islamabad by New Delhi and Tehran to act on terror safe havens in its territory but Pakistan continues to turn a blind eye on them.