The development comes after the Afghan Ambassador to Pakistan, Shukrullah Atif Mashal, had accused Pakistani police of attacking the market, which Afghanistan claims it, reports TOLO News.
According to reports, the ownership of the property is disputed, but the Afghan Embassy in Islamabad maintains that the market property belongs to the Afghan government.
The Afghan government stated on Friday that such actions were "irresponsible and insulting".
Over the past few days, Afghan government officials have claimed Pakistani police have repeatedly entered the market and removed the Afghan flag.
"Many soldiers came here, acting like terrorists. This is not acceptable. This is not good for improving relations between the two countries," said Mashal.
Afghanistan's Foreign Affairs Ministry in a statement said: "The government of Afghanistan reiterates that the Afghan legal evidence has not been addressed in the context of the Afghan market due to political motives of the Pakistani court. Therefore, the Pakistani court's decision does not convince Afghan judicial institutions.
A number of civil society activists gathered in front of the Pakistani Embassy in Kabul and shouted slogans against Pakistan.
"Our flag is our national identity, no one can disrespect our identity," said a civil society activist.
"An attack on the Afghan market is an attack on friendship between two nations, and an attack on good neighbourly relations," another activist added.
The Pakistani government has not responded so far.
( With inputs from IANS )