In a report to be published on Monday, Christian Aid said London had to reverse a recent trend of linking aid to the fight against "terror".
Lead author John Davison highlighted Afghanistan and Uganda as places where funds have been wrongly diverted.
"The giving of aid by the world's richest countries is ruled by the rhetoric of 'with us or against us'. This must not be allowed to continue."
Davison added it was dangerous to blur humanitarian aid for the world's poorest with the military activities of their governments.
Afghanistan and Uganda
Christian Aid cites two particular case studies.
It claims Afghanistan's $2.2bn in aid for 2004 is being diverted to military projects and emergency relief rather than long-term redevelopment.
"Afghanistan is all about the security situation. The priority on security is a US priority - the hunting down of the Taliban and al-Qaida."
He said aid workers were seen as agents of the US and were being killed. In recent months, at least 11 had died, including two during a targeted raid on their Kandahar office.
"The giving of aid by the world's richest countries is ruled by the rhetoric of 'with us or against us'. This must not be allowed to continue"
Davison said two-thirds of the country was now off-limits to UN staff and "reconstruction is just not happening".
Uganda, meanwhile, is heavily dependent on aid donations which make up more than 50% of its budget.
The country is the third-largest recipient of aid from the UK's Department for International Development (DFID) - receiving more than $100 million in 2002-03.
However, an 18-year-old war being fought between The Lord's Resistance Army and the country's government saw almost a quarter of the social services budget in 2002 being used to fund military operations.
Fighting is predominantly in remote northern districts of the east African country and has resulted in hundreds of thousands of people being displaced.
Villagers bear the brunt of the violence and in the worst recent attack, more than 200 civilians were burned, shot and hacked to death when the rebels attacked a refugee camp.
"The Ugandan conflict needs to be resolved, but not through a military solution. Military operations have made the situation worse. In the midst of that, a lot of the budget went to defence," Davison concluded.