The club's general manager says he is only interested in putting the club's best interests first after refusing to allow the striker to join Bayern Munich
The Poland striker looked destined to follow in the footsteps of Mario Gotze and leave BVB for the Bavarians this summer, but the Bundesliga runners-up have refused to sanction his departure.
That resulted in Lewandowski hitting out at the club last week, but Watzke remains satisfied that he has acted in the best interests of the team in keeping him at Signal Iduna Park.
"He was obviously referring to me,” he stated to WAZ. “I can fully accept that Robert is a bit frustrated. But I have got to make decisions for the good of this club."
Watzke then revealed he was surprised that Gotze opted to depart the club, while explaining the decision to spend big money on recruiting Henrikh Mkhitaryan from Shakhtar Donetsk.
"I was surprised at that time by Gotze's decision to leave the club, but not at his destination. We spent a lot of money on Henrikh Mkhitaryan because we needed an immediate solution.
"He is a combination of the long-term and the short-term at this day. We could not have gotten a player that would have taken another three years to develop after Gotze's departure."
Dotmund surrendered their Bundesliga title to Bayern last season but did reach the final of the Champions League, where they were beaten by their great German rivals.
However, Watzke has written off the chances of Jurgen Klopp's side repeating that feat next season.
"It would be completely unrealistic to believe we can manage the semi-finals or finals of the Champions League in 2013-14 again," he said.
"I have no intention to paralyse us by heckling at targets. We must remain realists. With increasing success we will no longer be everybody's darling in the coming years.