Mr Qadir (left) with delegation leader Yunus Qanuni
Haji Abdul Qadir, recently reinstalled as governor of several eastern Afghan provinces, left the summit near Bonn on Thursday at a key moment in the negotiations.
Observers say his departure, while important, is more of a symbolic blow than an obstacle to progress.
"It doesn't really affect the show, the show goes on," UN spokesman Ahmad Fawzi told a news conference on Friday.
Click here for a who's who of the Afghan power brokers.
A spokesman for the Northern Alliance delegation, which includes two other Pashtuns, said Mr Qadir was still in Germany and might still
return to the talks.
As he left, the brother of another prominent Pashtun leader arrived, meaning that ethnic representation on Friday remained unchanged.
Tensions within the alliance are one possible explanation being touted for Mr Qadir's move.
Speculation in other quarters suggests he could be trying to strengthen his position by publicly standing up for the Pashtuns.
Hazara unease
Mr Qadir is the brother of Abdul Haq, who was killed by the Taleban after returning to Afghanistan in the early days of the US bombardment.
He is one of the few members of his country's southern- and eastern-based Pashtun majority to have joined the alliance, which is dominated by northern Tajiks, Uzbeks and Hazaras.
His departure came amid complaints that other Afghan groups are also unhappy with the composition of the delegations in Germany.
One Hazara leader, Karim Khalili, said his people and another minority, the Uzbeks, should have more than one representative.
"The United Nations talks about the fair treatment of tribes, but itself commits an oppression," Mr Khalili told Reuters.
Forces loyal to both Mr Khalili and Uzbek General Abdul Rashid Dostum play an important role in the Northern Alliance, which with US backing has swept the country's former Taleban rulers from Kabul and large parts of the north.
The Northern Alliance has most seats at the talks in Germany, which are also being attended by representatives of the former king - himself a Pashtun - and two exiled Pashtun groups.
Pashtuns account for about 40% of Afghanistan's population, followed by Tajiks - the biggest group in the Northern Alliance - with 25%. Hazaras make up some 15%.