Dr. William Hamilton, who performed the autopsy, said the execution of Angel Nieves Diaz took 34 minutes — twice as long as usual — and required a rare second dose of lethal chemicals.
The autopsy showed the needles used for the injection missed his veins and went into the flesh in his arms instead, CBS News correspondent Kelly Cobiella reports.
Hamilton refused to say whether he thought Diaz died a painful death.
"I am going to defer answers about pain and suffering until the autopsy is complete," he said. He said the results were preliminary and other tests may take several weeks.
Meanwhile, a federal judge who imposed a moratorium on executions in California on Friday declared the state's method of lethal injection unconstitutional.
U.S. District Judge Jeremy Fogel ruled in San Jose that California's "implementation of lethal injection is broken." But, he said "it can be fixed."
California has been under a capital punishment moratorium since February.
That's when Judge Fogel called off the execution of rapist and murderer Michael Morales amid fears Morales or other inmates might suffer excruciating deaths in San Quentin State Prison's death chamber.
Bush created a commission to examine the state's lethal injection process in light of Diaz's case, and he halted the signing of any more death warrants until the panel completes its final report by March 1.
The governor said he wants to ensure the process does not constitute cruel and unusual punishment, as some death penalty foes argued bitterly after Wednesday's execution.
Diaz, 55, was put to death for murdering of the manager of a Miami topless bar during a holdup in 1979.
The medical examiner's findings contradicted the explanation given by prison officials, who said Diaz needed the second dose because liver disease caused him to metabolize the lethal drugs more slowly.
Hamilton said that although there were records that Diaz had hepatitis, his liver appeared normal.
Executions in Florida normally take no more than about 15 minutes, with the inmate rendered unconscious and motionless within three to five minutes. But Diaz appeared to be moving 24 minutes after the first injection, grimacing, blinking, licking his lips, blowing and appearing to mouth words.
As a result of the chemicals going into Diaz's arms around the elbow, he had an 12-inch chemical burn on his right arm and an 11-inch chemical burn on his left arm, Hamilton said.
Florida Corrections Secretary James McDonough said the execution team did not see any swelling of the arms, which would have been an indication that the chemicals were going into tissues and not veins.
Diaz's attorney, Suzanne Myers Keffler, reacted angrily to the findings.
"This is complete negligence on the part of the state," she said. "When he was still moving after the first shot of chemicals, they should have known there was a problem and they shouldn't have continued. This shows a complete disregard for Mr. Diaz. This is disgusting."
Earlier, in a court hearing in Ocala, she had won an assurance from the attorney general's office that she could have access to all findings and evidence from the autopsy. She withdrew a request for an independent autopsy.
David Elliot, spokesman for the National Coalition to Abolish the Death Penalty, said experts his group had contacted suspected that liver disease was not the explanation for the problem.
"Florida has certainly deservedly earned a reputation for being a state that conducts botched executions, whether its electrocution or lethal injection," Elliot said. "We just think the Florida death penalty system is broken from start to finish."
Florida got rid of the electric chair after two inmates' heads caught fire during executions in the 1990s and another suffered a severe nosebleed in 2000. Lethal injection was portrayed as a more humane and more reliable process.