Poland international Lewandowski has been Bayern’s top goalscorer in three of the last four seasons since joining the club in 2014.
He has also reached the 40-goal mark in each of the last three campaigns.
His exploits have helped the club extend their domestic dominance, winning four German league titles in as many years.
But local media reports say Lewandowski, whose contract at Bayern runs until 2021, has been eager to find newer pastures.
“There is nothing new with Robert. The status is that he will not leave the club because he’s our top striker.
“And certainly we don’t want to give him away and won’t give him away,” Kovac told Sky Sports.
“It’s true that Robert is thinking about playing somewhere else. Naturally, one thing is what he wants, the other is what we want.
“We are FC Bayern, we have a top striker. We certainly will not let ourselves be persuaded from the outside. That’s the way to do it.
“Robert has a contract… he will certainly stay here as long as possible.”
Former Eintracht Frankfurt and Croatia manager Kovac also said that he does not expect the transfer situation to hinder Lewandowski in the upcoming campaign.
“He is a professional and knows that he also has something to prove to himself and everyone else.
“He actually already knows this. But we will say it again, that he will also have to step on the gas,” Kovac added.
“He also wants to score goals and be successful. Robert Lewandowski stands for success and goals and he will prove that in the future.”
Bayern start their league campaign against Hoffenheim on Aug. 24.