"The team were suspended because of a debt. So long as they don't settle the debt they will not be able to play their domestic matches," Mestanza told Reuters.
The FEF posted details of the debts on their website, including money owed to former Deportivo players.
"Deportivo Quito's debts with the FEF and players Johnny Baldeon and Ebelio Ordonez total $207,517 and they must pay by this Friday to be able to play in the fourth round of the Ecuadorean Football Championship, Copa Credife 2010, or they will lose the points," the FEF said.
The club also face a sanction from Ecuador's tax authorities, who have closed their training complex over unpaid taxes, revenue authorities said.
The FEF suspension does not prevent Deportivo from playing in the South American Libertadores Cup.
They lost 2-0 away to Cerro of Uruguay two weeks ago and their next Group Five match is at home to Internacional of Brazil on March 11.
Deportivo beat Espoli 2-0 at home last weekend for their first win after two defeats in their opening three matches in the 2010 national championship.
Barcelona of Guayaquil, Ecuador's biggest club, were banned from playing their next home match anywhere within their province after fans threw objects on to the pitch and injured a linesman in their last game.
The club were also fined $2,000.
