"Regarding Hummels this is a non-story. There is absolutely nothing there," Watzke told Reuters in an interview, brushing off reports of an imminent deal.
Hummels has been the latest Dortmund player linked with a move abroad as the 1997 Champions League winners find themselves back in the European spotlight with their attractive, attacking game.
"I have no concern for the winter transfer window because a player with no contract can leave but it is us who decide if a player with a contract will leave or not and I think we made that position very clear in the (Robert) Lewandowski case," Watzke said.
Dortmund repeatedly refused to allow the Poland international, their top striker, to join Bayern Munich in the close season even though his contract runs out in 2014 and Dortmund risk missing out on a transfer fee. Hummels has a deal to 2017.
Watzke said a turnover of players was natural but Dortmund would make sure not to lose more than one key player per season.
"It was always one player we gave away every season not more. There is no club in the world that does not sell players and Bayern have been doing it successfully for 50 years," said Watzke.
"You cannot play 10 years with the same team. If you have confidence and are able to do something to plug the leaks then you can be successful. We have been taking decisions after carefully planning how we can improve."
Dortmund have lost several big names in recent seasons with Shinji Kagawa joining Manchester United, Nuri Sahin signing for Real Madrid before returning earlier this year, striker Lucas Barrios moving to China and Mario Goetze joining Bayern Munich.
"We replaced Nuri with (Germany international Ilkay) Guendogan and look where he is now, Lucas Barrios with Lewandowski, Kagawa with Marco Reus. We have been very successful in filling the gaps with a lot of quality," Watzke said.
New signing Armenian Henrikh Mkhitaryan has been equally successful this season in replacing Goetze.
Successful transfers have contributed to the 2012/13 record turnover of 305 million euros and a profit of 53 million, a club record for Germany's only publicly traded club.
"We said turnover has to be looked at in relation to the revenues from transfers. Without that the turnover was about 253-254 million euros," Watzke said. "That is also the aim for this year. Last season we reached the Champions League final and that is not something that happens every year.
"So if all goes well we are planning for a turnover of about 250 million and profit in single-million digits due to higher write-downs after we spent almost 50 million euro in new transfers. Write-downs are expected to increase by about 10-11 million euros."
Watzke has been critical of foreign investors pumping millions into Spanish and English clubs and said he was equally perplexed with the decision to award Qatar the 2022 World Cup, making a winter tournament for the northern hemisphere countries a possibility.
"It is clear that awarding the World Cup to Qatar was because of financial reasons and not because of the country's long football tradition," he said.
"I never understood this decision, from the very start. On the other hand maybe you do not need to understand everything, you just have to accept it.
"If the relevant bodies within FIFA took that decision you can be angry or can talk about it as much as you like but at the end of the day you have to accept the decision."