The warnings come as the country's loya jirga - or grand assembly - is meeting in Kabul to form its next government, but political wrangling has delayed its work and it may now extend its session until Monday.
United Nations officials say there have been attacks on aid workers, extortion of their supplies, the torture and rape of Afghan civilians, and a gang rape of an international aid worker.
One American aid organisation has already pulled out of northern Afghanistan.
Another agency is considering closing down, after it was attacked during factional fighting.
At the same time, delegates at the loya jirga in Kabul have complained of intimidation by some of the mujahideen factions.
Grave concern
The UN Special Representative in Afghanistan, Lakhdar Brahimi, has demanded urgent action from two leading factional commanders - General Abdul Rashid Dostum and General Atta Mohamed - to stop what he calls an alarming level of violence, lawlessness and intimidation.
Mr Brahimi has also expressed his concern to the newly elected Afghan head of state, Hamid Karzai, who has repeatedly said he will deal with abuses by warlords.
But both men, along with the American representative in Kabul, have spoken of the need to pursue peace rather than justice at the moment, says the BBC's Kate Clark in Kabul.
They do not want to risk fighting by trying to exclude the armed factions from power, she says, and it seems inevitable that the warlords will be in the next government, even if Afghan civilians fear and dread them.
Cabinet row
The formation of Afghanistan's next government has entered another turbulent stage in a row over who will fill key cabinet posts.
Mr Karzai says he may not have a list to put to the loya jirga, as members insist they choose the new government.
Under the UN-brokered peace accords the loya jirga must approve the structure of the next administration.
The assembly meeting is due to finish on Sunday, but long and fiery speeches have delayed its work and the session may go into Monday.
The new government will run Afghanistan for 18 months before general elections are held.