The chief executive told Kicker magazine on Sunday that “it was no joke” and “not a marketing move”.
Dortmund and Bolt are both sponsored by the same Germany-based sports goods company Puma, whose president contacted Dortmund to say that Bolt had asked about training with the team.
“We decided this some time ago,” Watzke said. “Puma CEO Bjorn Gulden, who is member of our board, has told us that Usain is highly interested in practising with us.
“For us that’s no problem. Our coach Thomas Tuchel likes the idea as well. Of course he won’t visit us in an important week with Champions League matches but maybe in the pre-season. We are delighted and take this as an honour.’
Asked if Bolt could have a future in Dortmund, Watzke replied: “We don’t even need to talk about it.”
Bolt’s love of football is well documented and the Jamaican is known to be an avid Manchester United fan.
The sprinter, who claimed three gold medals in Rio at the Summer Olympics, has previously outlined his desire to play for the Premier League side.
"For me, if I could get to play for Manchester United, that would be like a dream come true," he said. "Yes, that would be epic."