The striker is reportedly on the verge of signing a five-year deal with the Premier League side, having previously been strongly linked with a move to Liverpool.
However, speaking ahead of Leipzig’s Bundesliga match against Paderborn, Mintzlaff said that Werner’s £54m release clause has not yet been met.
“So far, Timo Werner has not drawn the clause, nor has a club sent a transfer contract,” he told Sky Germany.
“We haven’t had an exchange yet, so we have nothing to report. Timo Werner is an RB Leipzig player.
“It was important for us that we extended his contract, which we did last summer, because of course it is important for our young club that no player moves free of charge.
“Of course, there was this release clause that we put in the contract to give him the opportunity to take the next step. Now Timo Werner is sitting in the driver's seat, no longer us.”
If Werner’s move to Chelsea is finalised soon then there is a chance he could leave Leipzig before they play in the delayed Champions League quarter-finals, which are scheduled for August.
Mintzlaff says that remains up in the air, but Werner should certainly finish the Bundesliga season with Leipzig.
“If Timo Werner should change clubs, then we are sure that with the new, buying club we will first find the clause for him to end the Bundesliga season, whenever that is.
“We can only discuss when we know when the Champions League is going to take place. It won't be decided until mid-June.”