According to the paper, former UN officials, diplomats, lawyers, and the head of Human Rights Watch were among those who have raised serious concerns about the way Damascus appears to be directing the aid effort and benefiting from some of these deals.
Salman Shaikh, a Middle East specialist who has worked for the UN, said it was time for the secretary general, Ban Ki-moon, to intervene. "It's as serious as that," he added.
The UN said, according to the report said, "its work has saved millions of lives. But it concedes it can only stay in Syria with the approval of Assad, who has restricted which partners its agencies are able to work with".
"Our choices in Syria are limited by a highly insecure context where finding companies and partners who operate in besieged and hard to reach areas is extremely challenging," a UN spokesman said.
Analysis by the Guardian revealed UN agencies have been awarding substantial contracts to Syrian government departments and Syrian businessmen whose companies are under US and EU sanctions.
Documents show the World Health Organisation has spent more than $5 million to support Syria's national blood bank, which is being controlled by Assad's defence department, raising questions about whether blood supplies are reaching those in need or are being directed to the military first.
The UN's own procurement documents show its agencies have done business with at least another 258 Syrian companies, paying sums as high as $54m. Many are likely to have links to Assad, or those close to him.
"In the name of delivering aid to some needy people in opposition-held areas, the UN is subsidising the Syrian government's war-crimes strategy of targeting those same people," said Kenneth Roth, executive director of HRW. "That's hardly the tough-minded pragmatism that the UN claims is informing its aid efforts."
Antonia Mulvey, the founder and executive director of Legal Action Worldwide, said the UN's conduct was an example of "pragmatism versus principles playing out in a conflict. Upholding fundamental human rights loses nearly every time."
The UN aid operation in Syria is the most expensive and complex it has ever undertaken. It argues it has already saved millions of lives during the brutal five-year conflict. Privately, officials fear if they over-challenge Assad the UN will be thrown out of the country.
"Operating in Syria, with the conflict now entering its sixth year, forces humanitarians to make difficult choices," a UN spokesman said.
"When faced with having to decide whether to procure goods or services from businesses that may be affiliated with the government or let civilians go without life-saving assistance, the choice is clear: our duty is to the civilians in need."
