Many in Pakistan see the entry into Kabul of Northern Alliance forces as a betrayal by the United States.
Only three days ago, they say, President Bush appeared to be endorsing General Musharraf's call for the Northern Alliance to stay out of Kabul until a broad-based administration was in place.
A Pakistan Foreign Ministry spokesman warned that if the Northern Alliance was allowed to form a government in Kabul, the civil war in Afghanistan would continue, dashing all hopes of peace.
Ethnic ties
The dilemmas faced by the Musharraf government are manifold.
First, Islamabad sees the Northern Alliance, particularly the Tajik elements who have seized the Afghan capital, as a hostile force which has received military and diplomatic support from Pakistan's arch-rival India.
Then there is the concern that if the Pashtuns - who straddle the border with Afghanistan and make up 40% of that country's population - are denied a share in power, Pakistan may have to face the fallout.
Because it saw a belligerent and unfriendly India along its long eastern border, Pakistan's military and intelligence establishment invested heavily in the predominantly-Pashtun Taleban in order to ensure a secure western frontier.
This support was to the exclusion of all other ethnic groups.
There was little surprise then that anti-Pakistan slogans were raised as the alliance forces took Kabul.
Challenge ahead
In the coming days if a formula to include the Pashtuns in any Kabul administration is not quickly agreed, analysts fear that President Musharraf may be forced to re-think his policy yet again.
It is too early to say whether he will go as far as to provide active support to the anti-alliance forces.
But what is clear is that if political developments are again outpaced by military advances, a stable Afghanistan will remain elusive.
And this stability appears vital if an effective battle is to be waged against international terrorism.