Jean-Marie Guehenno offered a dire assessment of the difficult rebuilding process in Afghanistan on Friday, which he said could cost five times more than previously thought.
In a report to the UN Security Council, he said continuing insecurity was delaying reconstruction and wreaking havoc in much of the country.
In some border districts, the Taliban now have de facto control over administration, he said.
Suspected Taliban, al-Qaida and other figters have carried out attacks while factional guerrilla fighting has also added to the insecurity.
Guehenno suggested the multiethnic government system spelled out by the Bonn agreement, after the Taliban were ousted in 2001 by a US-led war, was at risk.
"Insecurity has without question slowed the delivery of reconstruction, if not outright prevented it in the most insecure areas"
UN peacekeeping official
"Many of the fundamental, structural causes of insecurity remain unresolved," he said.
"There are worrying signs that the political compact that has allowed the government to press ahead with Bonn in spite of the differences of its individual members may be weakening.
"Insecurity has without question slowed the delivery of reconstruction, if not outright prevented it in the most insecure areas."
Guehenno said the international community had underestimated the amount needed to rebuild the country, and echoed requests from the government for more money and peacekeepers.
Donors have pledged more than $4 billion in aid over five years but as much as $6 billion annually could be needed to get the country back on its feet.
"It is now clear that significantly greater resources are required," Guehenno said.
The report comes as the international community is being pressed for billions of dollars more to help rebuild Iraq.
President Karzai's writ hardly
extends past Kabul
The Security Council, which last week authorised international peacekeeprs to deploy outside the capital Kabul to restore order, will head to Afghanistan next week for a first-hand look at the situation.
Germany will send up to 450 troops to deploy around the northern city of Kunduz but there have not yet been commitments from other countries to commit to the international force.
"This is a Muslim country that wants more UN presence," said Heraldo Munoz, the UN ambassador from Security Council member Chile.
"They want more multilateral engagement and not less... The cooperation that they are asking for, I think, should be responded to positively."