In the past weeks hundreds of rebels have been killed. But so have scores of Afghans, including civilians, and 10 coalition soldiers have lost their lives in combat in just the past week.
Security forces say the increase in clashes is because they are penetrating lawless areas where the rebels have for years operated freely, sometimes teaming up with opium lords and other criminals.
But the rebels also appear to be finding some support in destitute remote areas where people are fed up with the killing, government corruption and lack of development, or are too afraid to resist.
Among those who live in the country Karzai’s administration appears increasingly weak.
"The state is fragile, the president is fragile and the system is fragile," political and legal analyst Waheed Mujda told AFP.
The policymakers of the administration, including from the international community that has been guiding and funding the country since the Taliban left, "are simply people who knew nothing about the reality of Afghanistan," he said.
Karzai has denied the resurgent militia are a threat but said the international community needs to find a better way to tackle the violence and that Afghanistan could not forever be a main theatre for the "war on terror".
There needs to be a more strategic approach to disarming "the terrorists by stopping their sources of money, training, equipment and motivation," he said.
Afghan officials say much of this support comes from across the border in Pakistan where they allege neo-Taliban are entrenching themselves despite the presence of 80,000 Pakistani troops.
The accusation, strongly denied by Islamabad, has led to a deterioration this year of relations between Afghanistan and Pakistan, which only abandoned its support of the Taliban — which it nurtured into existence in the early 1990s — after the September 11, 2001 attacks blamed on Al-Qaeda.
Rice’s main message in her short visit to both countries was that increased cooperation between them against the militants was necessary.