However, the leaders of two of Pakistan's seven tribal regions, North and South Waziristan, have already announced they will be boycotting the talks.
The Afghan foreign ministry said that Musharraf's decision not to attend would not affect the talks, but Karzai emphasised the importance of his counterpart's role during a telephone conversation.
"We believe the absence of President Musharraf, who is busy at home, won't effect the jirga," Sultan Ahmad Baheen, Afghanistan's foreign ministry spokesman, told one news agency.
A foreign ministry statement said that Musharraf had assured Karzai of his full support in making the talks a success.
Kamal Hyder, Al Jazeera's correspondent in Islamabad, said that diplomats believed that Musharraf's decision not to attend was due to 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.
|"This sudden development only goes to show how things have got worse between the allies in the war on terror"|
Talat Masood, Pakistan-based defence analyst
"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.
Waheed Omer, one of the organisers, told Al Jazeera that he had hoped bringing the two sides together would help find some real solutions to problems along the shared border.
"We are going to this jirga thinking that this terrorism is a threat to Afghanistan and it is a threat to Pakistan and it's an enemy for both so there won't be any blame games," he said.
Security will be tight for the event as officials fear an attack by Taliban fighters, who are not being allowed to attend. Nearly 2,500 police will guard the event, the Afghan interior ministry said.
The jirga was due to be attended by about 700 tribal representatives.