Sources inside the secretive Whitehall committee which makes recommendations on honours decisions told the Mirror Beckham had been given a 'red flag' by HM Revenue and Customs for his tax affairs in 2013.
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Beckham had previously hit the headlines after investing in the controversial Ingenious Media investment scheme, used by an array of wealthy stars to channel funds into tax-efficient arts projects.
The honours source said there was no suggestion any laws had been broken, but that the warning from HMRC was sufficient for Beckham to miss out on a knighthood at that time.
"For anybody who is being considered for an honour, we got advice on the reputational risk on relation to their tax affairs," the committee source said.
"It is ranked red, amber and green. And if it is red, the general rule is you do not give them an honour."
Beckham had been recommended for a knighthood in November 2013 by Olympics chief Lord Coe.
It followed his service for the England football team, tireless charity work over many years and key role in the success of the 2012 London Olympics.
The source said senior officials on the committee believed Beckham "deserved an honour" and went to "personal lengths" to try to solve the impasse.
But private talks with Beckham's camp failed to solve the issue raised about his tax arrangements.
(Beckham's) agent was aware of the issue holding it up," the honours source said.
"But you have got to have rules. And the general view of the committee was that people in the 'red' category do not get an honour."
Labour and Lib Dem MPs hit out at what they called a "bend it for Beckham" culture at the honours committee, raising concerns that officials had discussed Beckham's tax affairs with his agent.
Rosena Allin-Khan, Labour's shadow culture minister, said: "It's incredibly worrying if people who make the decisions on honours are offering advice to high profile celebrities."
Lib Dem MP John Pugh, a member of the Commons Public Accounts Committee, added: "No one should be above the law and everyone should pay everything they owe, but we shouldn't create a new 'bend it for Beckham rule' for certain people.
"All the charity work David has done, much of which is below the radar is more than enough for a major honour. The Tories hand gongs out to much less deserving people."
At the time of the dispute, the committee was chaired by Sir Bob Kerslake, who was then the head of the civil service.
He refused to comment last night, telling the Mirror: "I cannot comment on individual cases."