City released a statement following the initial allegations that were made on Friday.
City's Abu Dhabi owners are alleged to have reimbursed Fordham directly in a move which shaved millions off the club's wage bill and allowed them to report around £26m extra in marketing income.
"Our partnership with Manchester City and the broader City Football Group continues to deliver important ongoing and accumulative returns on our investments".
Der Spiegel has also claimed that City struck a deal with UEFA to avoid a Champions League ban when it was found they had breached FFP rules, and that a third-party company to which they sold player image rights was also funded by the Sheikh.
"We certainly hope Uefa will take the right decisions and enforce Financial Fair Play rules, but we don't have full confidence that they will".
Der Spiegel claims one of City's solutions to circumvent the rules was to launch Project Longbow.
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He said: "Everything went perfectly to plan, and she's been beaten by a great filly, with a great trainer and owner". Monomoy Girl bolstered her case as the top 3-year-old filly by winning the $2 million Distaff.
It created "Project Longbow", the name seemingly chosen because it was the weapon of choice for the English army against the French at the famous medieval battles of Crécy and Agincourt.
That included selling players' image rights to an external company, therefore writing off that cost from their accounts.
Man City has not disputed the authenticity of the documents, and said an "attempt to damage the club's reputation is organized and clear". This was followed up by further claims on Monday and Tuesday, including suggestions sponsorship deals with Abu Dhabi-based companies were topped up by discrete payments from City's owner Sheikh Mansour.
Documents leaked to Der Spiegel and other media from the Football Leaks' whistleblowing website purport to show the two clubs had inflated sponsorship revenues to meet FFP requirements. One memo from chief executive Ferran Soriano is said to have read, "We will need to fight this and do it in a way that is not visible, or we will be pointed out as the global enemies of football".
Der Spiegel calls the settlements "weak" and claims Uefa "wasn't even entirely aware of the degree to which it had been deceived". The leaks validate what we have been saying for more than a year.
Der Spiegel reports that, in an internal email, City's chief financial officer Jorge Chumillas wrote: "We will have a shortfall of £9.9m in order to comply with Uefa FFP this season". When auditors PricewaterhouseCoopers later reviewed the Fordham deal on behalf of UEFA, it was concluded that it was a "very good deal for MCFC", not least because the auditors couldn't figure out how Fordham expected to make any money on the deal for themselves.