The 23-year-old joined Leipzig from Stuttgart in 2016 and has since racked up over 100 appearances for the club while establishing himself as one of Europe's most deadly forwards.
Werner has hit 20 goals in 36 matches across all competitions this season, helping Leipzig secure a top-three spot in the Bundesliga and reach the DFB Cup final .
The Germany international has long been linked with a move to Bayern, with his current contract at the Red Bull Arena set to expire in 2020.
"We have not talked to Bayern about Timo Werner yet," Mintzlaff began. "It was important for us what Timo Werner wants.
"It was legitimate for a young player like Werner to spend time deciding on his future.
"Maybe Timo will tell us after the Cup final: 'Come on, I'll extend that by two more years'."
Bayern are on course to win the German title for a seventh consecutive year , holding a two-point lead over Borussia Dortmund heading into the final round of matches.
However, Niko Kovac's side have faced plenty of criticism throughout the campaign, with a number of veteran stars touted for summer exits.
Franck Ribery and Arjen Robben have already confirmed their departures, which leaves room for Werner to be drafted in to provide added depth up front.
Leipzig, meanwhile, can look forward to returning to the Champions League next season, after another successful year with Ralf Rangnick at the helm.
Mintzlaff went on to dismiss any suggestions the German coach could leave the club this summer, as he added: "Ralf Rangnick will stay with us, there is no question mark.
"We have no dissent at all, but have extremely harmonious and open discussions about the future."
Leipzig finish their Bundesliga campaign with a trip to Werder Bremen next weekend, before squaring off against Bayern in the DFB Cup final on May 25.