Parliament elections were held in September, the results of which were vigorously disputed for three months, pushing the country to the brink of a constitutional crisis.
Now, several Afghan officials and losing candidates have warned that the seating of the new Parliament could fuel the insurgency and even an ethnic strife that might lead to civil war.
"Step by step Pashtuns will say we are not represented, the government does not care about us, our people are not in government, and step by step they will join the enemy," the New York Times quoted Jamil Karzai, a former member of Parliament and cousin of the president, as saying.
He is among a group of some 80 losing candidates who are challenging the results.
President Karzai has stayed aloof from the dispute, but according to his chief of staff, Umar Daudzai, has been responsive to the complaints of some candidates of "fraud, misconduct and miscounting," as well as the greater concern of widening ethnic divisions.
Karzai has sent the complainants to his attorney general, who has already passed their case to the Supreme Court.
"We trust the Supreme Court will be responsive to their complaints," Daudzai said.
But few believe the Supreme Court can deliver satisfaction at this late hour.
A number of losing candidates are also blaming the president for allowing a decline in Pashtun influence, and warn that there is little hope for Afghanistan to achieve peace and security without incorporating the Pashtuns, who make up about 46 percent of the population, and have traditionally ruled the country. They also form most of the ranks of the Taliban.
The Pashtuns have lost at least 26 seats in the new Parliament - dropping from 120 to 94 in the 249-seat lower house.
"It is difficult for Karzai, and for NATO, too. For the country it is not good," said one senior government official. (ANI)