The FA could lose millions of pounds of funding if it does not reform, says Sports Minister Tracey Crouch.
Money will be given to other projects, and potentially county football associations, if changes are not made, she told BBC Radio 5 live's Sportsweek.
Crouch said: "I'm not shy to say to the FA 'if you don't reform your governance structures, I will give that money to other bodies that deliver football'."
She said the governing body receives £30m to £40m of public funding.
Earlier this month, former FA chairman David Bernstein said the organisation was "outdated" and needed reform.
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