The man later died of a heart attack, and the botched execution was expected to intensify the debate over how states handle lethal injections.
The White House said the failed execution fell short of the humane standards required when the death penalty is carried out.
Oklahoma Gov. Mary Fallin called for an independent review of the state's execution protocols.
The autopsy in Tulsa, Oklahoma, was expected to last for several hours, Elliott said, and it could take two to four months to complete the toxicology report.
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It is routine for the medical examiner's office to conduct an autopsy on inmates after an execution, but Lockett's death is unusual because his execution was halted before he was declared dead.
Lockett was declared unconscious 10 minutes after the first of three drugs in Oklahoma's new lethal injection combination was administered last evening. Three minutes later, he began breathing heavily, writhing, clenching his teeth and straining to lift his head off the pillow.
Questions about execution procedures have drawn renewed attention from defense attorneys and death penalty opponents in recent months, as several states scrambled to find new sources of execution drugs because drugmakers that oppose capital punishment many based in Europe have stopped selling to US prisons and corrections departments.