The midfielder's fitness issues have not deterred die Schwarzgelben from trying to extend the Germany international's deal, with a decision over whether he'll sign imminent
The midfielder, 23, has been linked with a move away from Signal Iduna Park over the past 12 months, with names such as Barcelona and Manchester United frequently popping up in reports, even though he has spent much of this season out with a back injury.
However, Watzke says his medical issues have not affected the club's desire for the Germany international to commit his future to the club.
"The fact that we would like to extend the contract of Ilkay Gundogan is clear," he told Sky Sport News HD. "But there's always more to it.
"We also have a certain degree of respect for his long medical history, which of course has charged him and is why he wants to look further into how his body can be kept fit.
"This will certainly not be a never-ending story. We will use the next few weeks together to make a decision and we are in contact with Ilkay and his family, who also advise him."
Gundogan has only played three competitive matches this season for Dortmund, having picked up his current injury last August when Germany faced Paraguay in an international friendly.