"The director of Spanish National Radio (RNE), given the controversy and annoyance caused be the programme, has removed this episode from the Internet," a spokesman for the broadcaster, Carlos Garrido, told AFP on Thursday.
The management of the station also apologised to the former spokesman for Israel's foreign ministry, Yigal Palmor, who "raised the problem" in an article in the Jerusalem Post, he added.
The spokesman stressed that the programme was "radio fiction and in no way was a news segment."
The half-hour programme "From the Inferno", which has been broadcast since 2009 in the early hours of Saturday, deals with myths about the devil throughout the ages. Episodes have dealt with devil myths in the Third Reich in Nazi Germany and during the Iraq war.
The episode which sparked the controversy, called "The Jewish People: Propagator of the Satan Cult", was broadcast on July 25th.
The Anti-Defamation league, a New York-based organisation that fights anti-Semitism, said the broadcast included "slander" of Judaism lifted from the "Plot Against the Church", a book published in 1962 "filled with anti-Semitic rhetoric" that was written by a collection of Mexican priests under the pseudonym Maurice Pinay.
"The fact that a vehemently anti-Semitic work filled with anti-Semitic conspiracy theories and slander made it to the Spanish airwaves is seriously troubling and warrants immediate condemnation from the Spanish government," the national director of the league, Jonathan Greenblatt, said in a statement.
Greenblatt wrote to Spanish Foreign Minister Jose Manuel Garcia-Margallo to urge Madrid to publicly condemn the broadcast.
"Strong action will convey the seriousness of the government's commitment to combat anti-Semitism and, we hope, deter future incidents," he wrote in the letter.