The letter said that an invitation from Khan for a Taliban delegation to travel to Pakistan for talks "amounts to the official recognition and legitimization of an armed-group that poses a serious threat to the security and stability of Afghanistan, and whose members are sanctioned by provisions of the UN Security Council's 1988 Committee's Sanctions Regime".
The announcement came hours after Afghanistan issued a protest to the UN Security Council over the planned visit.
The letter says that Taliban pose threats to Afghanistan's peace and stability and that nine members of the Taliban delegations are on the United Nations sanctions list and that the reports of the Taliban visit to Pakistan is a matter of concern for the Afghan government and the people.
"The Islamic Emirate had planned participation of its members in talks with United States negotiating team in the Pakistani capital of Islamabad which has been postponed due to inclusion of most of the members of our negotiation team in black list maintained by the U.S. and the UN", a Taliban statement said.
On February 13, Taliban said that a negotiating team of Afghan Taliban will be visiting Islamabad next week to hold another round of negotiations with the officials of the US.
"These engagements, which are taking place under the pretext of support for peace efforts in Afghanistan, are void of any degree of coordination and consultation with the government of Afghanistan", it said.
A Taliban statement said the negotiation team to be led by Sher Abbas Stanekzai also includes five senior members who were freed from the American prison at Guantanamo Bay in 2014.
Incidentally, the letter by Afghan government to the UN Security Council was despatched ahead of Saudi Crown Prince Md Bin Salman's proposed meeting with the Taliban delegation in Islamabad on Monday.
Taliban officials say they want all foreign troops out before a ceasefire, but would still welcome non-military foreign help to re-build the country.
But tensions run high between Afghanistan and Pakistan. Pakistan denies the allegations.
Now the next round of talks between rebel and United States will be held on February 25 in Doha as panned earlier.
Representatives of the Taliban attend worldwide talks on Afghanistan in Moscow on November 9, 2018.
A US team led by US Special Representative Zalmay Khalilzad has been negotiating with the Taliban representative to put an end to the 17-year-old war in Afghanistan.
It is also pushing hard for the Taliban to talk to the Afghan government, which it has so far shut out of talks, branding it as a puppet of Washington.