Kushner's comments come just days after Uefa asked a court in New York to approve subpoenas for testimony and documents from both the financier and Thrive as it considers lodging a criminal complaint against Infantino in Switzerland.
European football's governing body Uefa has led the rebellion against the Fifa president, who is facing calls to stand down.
In a statement, Kushner said: "Money in football has historically been concentrated amongst a small group of countries.
"The idea behind FFE was to direct more capital and equity equally amongst all 211 member countries, providing significantly more investment to underdeveloped nations to nurture local talent, support grassroots football, enhance the fan experience, and ultimately grow the global game everywhere.
"It was an idea that every member association would vote on, not an obligation or determination.
"While we stand behind the motivations of FFE, we failed to appreciate the political dynamics of global football, and the lengths some would go to. Thrive has a long track record of being a partner to all constituents. Had we known what this would devolve into, we would not have gotten involved."
Uefa's lawyers have also lodged legal papers asking for disclosure of documents from two Fifa businesses in the US and American financier Greg Maffei, who was described as a key adviser on the deal.
While Uefa has made clear that neither Kushner nor Maffei are anticipated defendants in any legal proceedings, its court submission claims that Infantino, "unilaterally designated Thrive Eternal…to lead the investor group".
Its lawyers also argue the World Cup was deliberately undervalued at around £15bn, which it says is "a figure that was neither the product of an open, competitive auction, nor tested by any independent valuer". It claims Infantino failed to consult Fifa's hierarchy over the plan.
Kushner has recently agreed a deal to buy basketball's Los Angeles Lakers for a record $12.5bn (£9.3bn).

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