Tasnim Aslam, the foreign ministry spokeswoman, on Saturday refused to give the nationality or identity of the alleged mastermind, and said the disclosure was not meant to shift responsibility onto Afghanistan.
"Afghanistan is also suffering because of al-Qaeda terrorism," Aslam said. "But what we have stated, we stand by it: We have evidence that suggests that the plot was hatched by Afghanistan-based al-Qaeda."
Afghanistan has accused Pakistan of making the claim as a diversionary tactic. It blames Pakistan, where at least seven suspects in the aircraft plot have been arrested, of not doing enough to crack down on terrorists operating on its soil.
Aslam's comments follow accounts from Pakistani intelligence officials that an al-Qaeda leader based in Afghanistan's eastern Kunar province masterminded the plans to blow up US-bound jetliners.
The officials allege the mastermind was in touch with Rashid Rauf, a Briton arrested in Pakistan and identified by the government as a "key person" in the plot.
Rauf recruited would-be bombers to take part in a large-scale attack to mark the fifth anniversary of the September 11, 2001, terrorist strikes in the United States, the officials claim.
"Somebody pretty high up in the al-Qaeda organisation was behind" the plot, Aslam said, without elaborating.