Wijetlaka, 64, was arrested on Wednesday night at his apartment on the Upper East Side.
He is charged with illegally distributing prescription pain medication. Authorities were searching his office for documents, including billing records.
According to the criminal complaint, investigators were working with an informant who said he received prescriptions from Wijetlaka even though he was not evaluated by the doctor.
Investigators also charge that Wijetlaka continued to write prescriptions even after his license was revoked.
A state board revoked Wijetlaka's medical license last month, citing him for gross incompetence.
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