However, the leaders of two of Pakistan's seven tribal regions, North and South Waziristan, have already announced they will be boycotting the talks.
Kamal Hyder, Al Jazeera's correspondent in Islamabad, said that diplomats believe Musharraf's decision not to attend comes from his domestic problems.
"Diplomats will tell you that the president has other serious issues to deal with - his re-election, the political instability within Pakistan, and the ongoing deal with Benazir Bhutto. That would be the reason [for the absence] from the Pakistani side.
"A lot of the tribal leaders said that they would not go to Kabul simply because if their own house was on fire, they did not see the point of bringing peace to Afghanistan.
"There was a lot of scepticism about the jirga in Kabul, and now that the president has pulled out, there has been a wave of speculation about it."
Talat Masood, a Pakistan-based defence analyst, said: "This sudden development only goes to show how things have got worse between the allies in the war on terror."
Musharraf has been under pressure to control the tribal regions, and has been angered by accusations from Washington that his country has become a safe haven for al-Qaeda and a regrouped Taliban.
The jirga was due to be attended by about 700 tribal representatives.