Instances have included a gang rape of an international staff member, break-ins at two NGO offices and NGO vehicles being fired on.
"It is becoming almost impossible for many NGOs to work effectively in northern areas," said a spokesman at the Agency Coordinating Body for Afghan Relief, which represents 60 NGOs in the region. "Every time a convoy with relief goods goes out, it risks being hijacked. Every agency that brings in money for salaries, or for running employment schemes risks being looted."
At the end of last month, aid agencies, including Afghan Aid, Christian Aid, CARE, Oxfam and Save the Children UK, got together to press the United Nations Security Council for an extension of the peacekeeping force in the north of the country. In addition a letter has been sent to defence secretary Geoff Hoon calling for further security measures.
Factional fighting has led to homes being burned and families displaced, according to the Security Council letter, which says that some NGOs have terminated operations and several more are "strongly considering withdrawal".
Some agencies are keeping female staff confined to headquarters and most are operating curfews.
"The increase in targeted violence stems directly from the security vacuum in the north,
said Vikram Parekh, a researcher with monitoring group Human Rights Watch. "Expanding the International Security Assistance Force is vital to the security of Afghan civilians and aid groups."
However, differences have emerged between aid agencies and field workers on whether military expansion is the best way to solve the problem. While some aid agencies are taking a strong stance, some field workers are wary of imposing an international solution on a local problem.
A spokesman for Oxfam said: "The UK government said that it would be prepared to consider deploying additional British troops in an emergency. NGOs in Afghanistan regard the situation in the north as an emergency."