In the letter to the UN Office for the Coordination of Humanitarian Affairs (OCHA), the 73 signatories demanded an investigation of the UN agencies' work in Syria and called for a monitoring body to be set up to oversee the relief effort.
"It has become clear to many organizations that the Syrian government in Damascus has a significant and substantial influence on the performance of UN agencies based in Damascus as well as their partners," including the Syrian Arab Red Cross, said the letter.
The groups announced they were pulling out of a UN information-sharing program for aid deliveries and would propose a new mechanism "where there is no political influence in any aspect of it."
"The Syrian government has interfered with the delivery of humanitarian assistance in multiple instances," the aid groups wrote.
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They took aim at the failure of the United Nations to deliver aid to nearly 600,000 people living in besieged areas, most of which are surrounded by President Bashar al-Assad's forces.
The newspaper's analysis of hundreds of UN contracts granted since the Syrian conflict began in 2011 showed many awarded to companies run by or linked to regime players who are under US and EU sanctions.
But the United Nations defended its actions, saying it had to work with the Syrian government to ensure aid deliveries.
The Guardian found that two UN agencies had partnered with the Syria Trust charity, an organization started and chaired by Assad's wife Asma, spending a total of $8.5 million.