Merkel told ZDF television on Thursday that the council, which advises her on questions regarding technology, would be replaced by "two different institutions." The German media reported this week that the conservative chancellor was looking to relieve von Pierer of his duties at the council.
Merkel did not elaborate on her decision and a government spokesman would only say that the next meeting of the council was due to take place on April 28.
Von Pierer, who was chief executive of Siemens from 1992 to 2005 before becoming head of the group's supervisory board, stepped down last year amid an investigation into corruption at the engineering giant.
Siemens has been caught up in a scandal that centers on a slush fund allegedly used to pay bribes in exchange for foreign contracts. Prosecutors in Munich said earlier this month that an investigation had cleared von Pierer for now but added that the probe continued.
"The enquiry shows for now that Mr. von Pierer had not been informed of misbehaviour within the company," chief prosecutor Anton Winkler said.