Bayern, treble winners last season, are 20 points clear at the top with Dortmund in second place and the title race all but finished after 23 matchdays with 11 left to play.
"I respect the work of Bayern a lot but that does not mean that we - as well as the other Bundesliga clubs - have only got to send letters of submissiveness to Munich," Watzke told sportbild magazine.
"We have the task of beating Bayern on occasion. We should not hang our ambitions to beat Bayern at the cloakroom."
Bayern have been unbeaten in the Bundesliga for more than 16 months with their last loss dating back to October 2012.
With another record-breaking run this season Bayern are on track to defend their German league and Cup titles.
They also beat Arsenal 2-0 last month in London in their Champions League round of 16 first leg tie as they seek to become the first team to successfully defend that trophy.
Their dominance - financial and sporting - has resulted in the Bavarians being accused of creating a "boring" league with some clubs resting key players against Bayern to keep them fit for other games they feel they have more chance of winning.
Schalke 04 coach Jens Keller even joked ahead of their 5-1 demolition by Bayern last week that he would put the team bus in goal to avoid a thrashing.
"Such comments are not helpful," said Watzke, whose club won the league in 2011 and 2012 and lost the 2013 Champions League final to Bayern.
"Club officials should not appear to be so submissive. I am convinced players register such comments.
"No courage is created if one is just happy to have gotten an invitation to the Kaefer (Munich restaurant)," Watzke said.
- Sports & Recreation