The man, named only as Saleh, worked as a translator for Mohammed Emwazi in Syria and spoke of the power the Briton wields over his fellow militants.
The 26-year-old Londoner was unmasked as the man who appears in most of the IS video's showing the beheadings of Western hostages.
Kenji Goto was murdered by Islamic State in January despite intense negotiations for his release.
Saleh told Sky News: "When he [Jihadi John] killed Kenji Goto I live showed this [saw this] but not near, from a little [distance].
"After he was killed him, three or four person come and take over the body and put in a car. After that, John went on a different road.
"The big boss was there with them. Turkish man say 'put this camera there, change place there' but John [was] the big boss. All time, all time say to all 'fastly, fastly, fastly, we should finish'. So respect him. Only he talks orders - others do."
The defector suggest Emwazi had respect amongst other jihadis because of his willingness to kill and appear in propaganda videos, "maybe because he use the knife," he said
"I cannot understand why he is so strong. One man can kill and all people will respect. A Syrian man anyone [in IS] can kill. But strangers [foreigners], only John."
Saleh told Sky News that there were often 'mock killings' where beheadings were rehearsed.
"He would say to me 'say to them, no problem, only video, we don't kill you, we want from your government [to] stop attacking Syria. We don't have any problem with you; you are only our visitors'.
"So they don't worry. Always I say to them 'don't worry, doesn't matter, nothing dangerous for you. But at the end I was sure [they would die]."
A warning - you may find some of the details in this report upsetting: