Bayern chief executive Karl Heinz Rummenigge is understood to have informed Scholl that he must choose between the two roles, with his focus apparently compromised.
"At one point, he must choose his path: coach or consultant. Both do not agree," Rummenigge told Sport Bil.
"When the TV contracts (for) Scholl expire, they should not be extended.”
Scholl is understood to have a contract with ARD which runs until the end of the World 2014 in Brazil.
Rummenigge has previously expressed his displeasure with Scholl, who openly criticised Bayern striker Mario Gomez and the national team during Euro 2012 in July.
The 41-year-old represented Bayern between 1992 and 2007, during which he won five titles and eight cups and triumphed in the Champions League in 2001. He also picked up 36 caps for Germany and won the Euro in 1996.
Scholl has been the Bayern youth coach since 2008, and took command of the reserve team in 2009.