The call comes amid increasing criticism of the international troops fighting Taliban insurgents, with scores of civilians, including women and children, perishing as a result of their operations.
"We strongly condemn the operations and force protection measures carried out by international military forces in which disproportionate or indiscriminate use of force has resulted in civilian casualties," read a statement released by the Agency Coordinating Body for Afghan Relief (ACBAR), an umbrella of more than 90 humanitarian and development NGOs.
The statement holds Afghan and international forces responsible for at least 230 civilian deaths, including 60 women and children, in their military engagements in 2007 alone.
"Fourteen civilians have been killed for simply driving or walking too close to international military personnel or vehicles," the statement said.
On 17 June, US warplanes bombed a religious school in Zarghun Shah District of western Paktika Province, killing seven children aged 8 to 15, a US military press release said. US forces have blamed Taliban and al-Qaeda for the unfortunate incident.
"This is another example of al-Qaeda using the protective status of a mosque, as well as innocent civilians, to shield themselves," read a press release, issued on 18 June from the US military base at Baghram airfield.
The NGOs urged the international forces to comply with international and Afghan laws, and respect local culture while conducting house searches and arrests.
The NGO association, which includes many Western humanitarian organisations, said Afghan support for international military forces had "substantially diminished".
"Excessive and disproportionate use of force is not only illegal and wrong but is also counter-productive," the NGOs said.
NATO-led International Security Assistance Force (ISAF) and US troops operating under Operation Enduring Freedom (OEF) command in Afghanistan rejected the criticism.
"We have always respected international law in our military engagements and have worked alongside Afghan forces," said Maj Chris Belchera, a US military spokesman at Baghram airfield to the north of the capital, Kabul.
A spokesman for ISAF in Kabul, Maj John Thomas, gave a similar account, adding NATO would do its best to reduce civilian casualties in its operations.
"Sometimes we even call off air strikes to avoid unnecessary harm to noncombatants," Thomas said.
However, Matt Waldman from a British charity organisation, Oxfam GB, called on the US military to do more for the safety of civilians in Afghanistan.
Hundreds of civilians have died in numerous suicide and roadside explosions carried out by the Taliban and their allies.
On 15 June, a suicide bomber blew himself up in Tarinkot, the provincial capital of southern Urozgan Province, killing one soldier and 11 children, according to the UN.
Sources associated with Taliban rebels claimed responsibility for the attack but blamed soldiers for choosing to patrol where children were playing.
Members of ACBAR have, furthermore, asked Afghan and international forces, including all American armed units in Afghanistan, to establish a permanent body for better coordination and common standards of operation.
NGOs have indicated that many incidents in which unarmed Afghans have been affected by military operations are caused by inaccurate or false information.
Afghan, OEF and NATO forces, however, say their efforts are already well coordinated.
Thomas said ISAF maintained good coordination with Afghan and OEF forces on a daily basis: "We work together on tactical and operational levels."
Waldman calls the current level of coordination between NATO, OEF and Afghan forces "insufficient" and, according to him, in need of urgent improvement.
Based on a strategic partnership signed by Bush and his Afghan counterpart Karzai in May 2005, US troops have freedom of action in all military operations in Afghanistan.
The ACBAR network of NGOs has called on the United Nations Assistance Mission for Afghanistan (UNAMA) and the country's human rights commission (AIHRC) to investigate every incident in which armed conflicts affect non-combatants - with the aim of verifying conflicting pieces of information.