Low had hinted ahead of Germany's World Cup qualifier against Ireland in Dublin that he did not consider the 24-year-old’s best position to be left-back.
The German manager said Schmelzer did not have a good game against Austria and they would work with him while looking at alternatives.
"Schmelzer did not have a good game. Many of the alternatives are not ready, we have to keep working with Schmelzer for the next two, three, four or five months,” he said.
These comments were not shared by Watzke who praised Schmelzer’s contribution to BVB and said he has proved his class internationally.
“Marcel gets any support from us. Even though in view of his achievements, he really doesn’t need it,” he said.
It’s not the first time there has been a disagreement between BVB and Low. The German national manager has been critical of Dortmund’s defenders in the past with Matt Hummels coming in for criticism following die Mannschaft’s Euro 2012 semi-final exit to Italy.
Watzke claims there is no ill feeling on his part towards Low and everything handled from their end via the media has been correct.
He added: "I just know that our behaviour towards the national team has always been extremely exemplary. From our side there was never criticism, certainly not through the media."