Health officials say six reported cases of hepatitis can be traced to the surgical center.
Officials are urging another 40,000 people who received treatment at the center over the past four years to get tested for the blood-borne virus, as well as HIV.
They say the clinic put patients at risk by reusing syringes and vials of medication.
Mayor Oscar Goodman says the clinic's business license will be suspended until further notice.
The four doctors who are named on the license can appeal the decision to city staff and, ultimately, to District Court.
A spokeswoman for a public relations firm representing the Endoscopy Center says she could not comment on the closure on advice of legal counsel.