The governing body said it had been "deliberately misled" by the club about a deal to sell player transfer fee rights to an outside investor.
FC Twente says it will not appeal.
Fifa has banned third-party player ownership as a threat to the game's integrity because investors can inflate transfer fees to make a profit.
The Dutch FA says the punishment, including a 45,250 euros (£34,000) fine, follows Twente's failure to reveal full details of a third-party ownership contract with Malta-based Doyen Sports Investments.
The Enschede-based club won their only Dutch League title under Steve McClaren, now the Newcastle boss, in 2009-10 but are currently third from bottom in the Dutch Eredivisie.
FC Twente said that the sanctions would "hit hard at the heart of our club".
Twente's professional licence will be revoked if they fail to fully cooperate with an independent investigation into the club's structure, added the Dutch FA.
FC Twente have been banned from European competition for three years by the Royal Netherlands Football Association.