A direct endorsement by hundreds of tribal representatives has given Karzai the much-needed legitimacy. He is no more a leader selected by a U.N. conference, as he was before the tribal council. He is now a leader elected by the powerful tribal chiefs of Afghanistan and their representatives.
But the process also weakened him by further strengthening the country's warlords. As Vikram Parekh of Human Rights Watch points out, the warlords also emerged from this exercise "with greater power and a new claim to legitimacy."
And they wasted no time in showing their new strength. Last week, troops loyal to the former Interior Minister Yunus Qanooni refused to accept their new boss, Haji Taj Mohammed Wardak.
Karzai had replaced Qanooni with Wardak to give more representation to his own ethnic group, the Pashtun, which is also the largest in Afghanistan. Qanooni belongs to the second-largest ethnic group of Tajiks.
When Karzai took over as the head of the interim Afghan administration in December, he gave all three key ministries of defense, interior and foreign affairs to the Tajiks. He had little choice because the portfolios were decided in the U.N.-sponsored Afghan peace conference in Germany in early December.
Since the same conference had selected Karzai as the head of the new administration, it would not have been politically prudent to change its arrangements. So throughout the six months that the interim administration ruled Afghanistan, Karzai patiently faced Pashtun criticism for allowing the Tajiks to dominate the government.
But the loya jirga process increased Karzai's confidence. He labored hard to ensure a high Pashtun participation in the tribal assembly and succeeded in gathering a large number of Pashtun representatives from across the country.
Describing it as one of the most extraordinary events in the recent Afghan history, Omar Zakhilwal, a Pashtun delegate to the jirga from Ottawa, says that during the first few days the delegates were focused on "national unity, peace and security."
But Pashtun delegates complain that soon security agents from the interior ministry took over the jirga. According to a Human Rights Watch report, issued on June 20, they controlled the microphone and prevented "independent and reform-minded delegates" from addressing the sessions. Those demanding more representation for women were particularly targeted, the report says.
To make the reformists ineffective, the warlords used an old strategy that almost always works in the Muslim countries. They brought in the clergy and got an edict from them, declaring the reformists "atheists and Salman Rushdies imported from the West."
The charge was taken so seriously that the newly appointed Afghan Supreme Court dragged the former minister for women affairs, Sima Samar, to the court where she had to prove that she was "not a Salman Rushdie."
This made it impossible for Karzai to include her or any other reform-minded woman in his government, despite pressure from the Western donors to give more representation to women.
Pashtun delegates also accuse the United States, Britain and other members of the U.S.-led alliance against terror of allowing the non-Pashtun warlords to dominate the jirga and the transitional government.
Independent observers say that it would have been difficult to prevent the warlords from dominating the interim administration formed in Bonn, as they were the only dominant force in Afghanistan after the collapse of the Taliban,
"But the selection of the transitional government to lead Afghanistan during reconstruction, by the delegates of the emergency loya jirga was supposed to reflect the voice of civilians, not warlords," says the Human Rights Watch report.
Pashtun delegates were also disappointed with the jirga's failure to give any formal role to the former king, Mohammed Zahir Shah. Although an ethnic Pashtun, the ex-king is generally accepted in Afghanistan as a symbol of unity and both Pashtuns and reformists believe that he could have been effective in countering the warlords had he been given a formal role.
Consequently, in the government that emerged out of the jirga the key ministries of defense and foreign affairs remained in the hands of Gen. Mohammed Qasim Fahim and Abdullah Abdullah, both from the dominant Northern Alliance faction.
Qanooni, the Northern Alliance's third key minister in the interim administration, was switched from the interior ministry to education but he did not accept this change until he was also given the post of a security adviser to the president.
The new post ensures his continued influence over the troops of the interior ministry who had already refused to accept Wardak. With Qanooni as Security Adviser, the powers of the interior minister will further be reduced.
All three vice presidents -- Fahim, Haji Abdul Qadir and Karim Khalili -- are also from the Northern Alliance. One of them, Qadir, is a Pashtun who had joined the Northern Alliance after the Taliban captured his eastern Ningarhar province.
"They represent the forces responsible for countless brutalities under the former mujahedin government," says Zakhilwal.
The new government, however, also includes some respected professionals like Finance Minister Ashraf Ghani and Minister for Mines Juma Mohammed Mohammadi but as a spokeswoman for the Revolutionary Association of Afghan Women points out, "they may or may not be able to influence the policies of the new government."
Since in Afghanistan, where more than 20 years of war has destroyed all civic institutions, it is those who hold the guns run the show. "And that's why the Northern Alliance has always been interested in the defense and interior ministries," says the RAWA spokeswoman.
Within the Northern Alliance, the Jamiat-i-Islami party of former Afghan president Burhanuddin Rabbani holds three key cabinet posts and the Shiite Hizb-i-Wahdat has one a seat.
Rights groups say that both parties have been implicated in the recent attacks on ethnic Pashtun civilians in northern Afghanistan following the collapse of the Taliban. Jamiat has also been involved in an ongoing conflict with Gen. Abdul Rashid Dostum's Junbish party in northern Afghanistan, where fighting and general insecurity have imperiled international humanitarian aid operations.
Saman Zia-Zarifi, a senior researcher at Human Rights Watch, blames both the international community and the interim administration for the failure of "the democratic and reform-minded people in having a say in the jirga."
"The absence of an internationally enforced security arrangement allowed the warlords to use the 6-month interim period to rebuild their military and political networks," says Zia-Zarifi. "It also prevented a civilian leadership from taking roots."
According to Zia-Zarifi, the reformists tried to submit a list of candidates for the transitional government but abandoned their plan after "three members of the group received death threats over the phone."
Incidents like this show the inherent weakness of the loya jirga process and Karzai's inability to use the assembly for putting together a government which can lead Afghanistan to a new and peaceful future.
But there is still hope, both for Karzai and Afghanistan. During the interim period, Karzai established himself as an honest and able politician; someone the international community can trust with the task of rebuilding the war-ravaged country.
The reconstruction of Afghanistan is a major concern for the international community. There is a general consensus that unless Afghanistan is helped to rebuild a viable economy, terrorism will continue. But the world leaders also understand that they need an honest and effective leadership to achieve this objective and they see Karzai as someone they can trust with this task.
This is something the warlords also seem to know. They realize that without U.S. help they could not have dislodged the Taliban government. They understand that there are forces in the country who are not happy with the current situation and if the U.S. support is withdrawn, the Northern Alliance may not be able to keep Kabul for long. And that's why they will not like to challenge someone who enjoys Washington's confidence.
During the last six months Karzai also has emerged as a leader acceptable to most Afghan factions. This general acceptance, and the support of the international community, can still be used to build a future for Afghanistan but for this Karzai has to try harder.