While the former Cardinal Joseph Ratzinger has possessed an organ donor card since the 1970s when he lived in Germany, it was rendered void when he became pope in 2005, his secretary said.
Monsignor Georg Gaenswein addressed the issue in a letter to a German doctor who has been using the fact that Benedict possessed a donor card to recruit other donors. Vatican Radio reported on the letter in a German language broadcast this week.
Gaenswein sought to put the matter to rest, saying any references to the now invalid document are mistaken.
Polish Archbishop Zygmunt Zimowski, head of the Vatican's health office, told La Repubblica newspaper that it was understandable that a pope's body remains intact because it belongs to the entire church.
"It is also understandable in view of possible future veneration," he said, referring to future sainthood. "This doesn't take anything away from the validity and the beauty of the gift of organ donation."
In a 2008 speech, Benedict lamented the shortage of organs for transplants, but denounced any selling of organs as immoral.
Until the last century papal organs were removed - not for transplants but to make embalming more durable.
The organs of 22 popes are preserved as relics in the church of Saints Anastasio and Vincent near the Trevi Fountain in Rome. The custom of removing the organs was abolished by Pope Pius X in the early 1900s. The collection includes the liver, spleen and pancreas of the popes.
When Pope John Paul II died in 2005, the Vatican denied that some of his organs would be sent to his native Poland as relics. He is buried at the Vatican.