Heynckes has endured a miserable 2012 so far with Bayern struggling domestically and 1-0 down to Basle in the Champions League second round.
“Those in charge of Bayern Munich condemn this outrageous media speculation, which is not based any facts, in the strongest possible terms,” said the Bavarians in a statement.
“We protest against this type of gossip journalism, which we will examine legally and take action against.”
“Bayern Munich have the fullest trust in Jupp Heynckes and his work.”