Ukrainian Emergency Ministry spokeswoman Nataliya Bystro said Sunday that recovery workers in the rebel-held territory had been laboring under duress and were forced to give the bodies to the armed gunmen.
"Where they took the bodies — we don't know," Bystro told The Associated Press.
Separatists were not immediately available Sunday morning to comment on her statement.
News reports of how the bodies had been decaying for days in the summer sun had ignited outrage worldwide, especially from the Netherlands, home to over half the victims.
Alexander Pilyushny, an emergency worker combing the crash site for body parts Sunday morning, told the AP it took the rebels several hours to take away the bodies on Saturday. He said he and other emergency workers had no choice but to hand the bodies over to the rebels.
"They are armed and we are not," Pilyushny said. "The rebels came, put the bodies onto the trucks and took them away somewhere."
Neither Bystro nor Pilyushny could explain what happened to the 102 bodies of plane victims that have not yet been recovered.