Lewandowski scored his 50th goal of the season across all competitions as Bayern capped off another successful Bundesliga campaign by drawing 2-2 at Wolfsburg on Saturday.
However, it was revealed before the match that the 33-year-old had refused the offer of a new deal.
Lewandowski is under contract until the end of next season but wants a new challenge after eight years with the Bundesliga giant. Barcelona has been heavily linked with making a move.
While Nagelsmann acknowledged it will be a loss whenever Lewandowski does leave Bayern – the club must decide whether to cash in over the coming months or instead keep him for next season and allow a free transfer – he insisted there is no time for sadness.
Instead, he must focus on the task of finding a replacement for a player who has broken countless records.
Nagelsmann said: "Yes, it is or would be a loss, but he still has a contract until 2023, and I think we have all already commented on this.
"There is also no other statement about it, except that he has a contract until 2023. There is really nothing more to report.
"Of course, it's always the case that if you lose a very good player, or lose a player in general, then it's always not nice. 'Sad' is maybe the wrong word, there are other things in life to be sad about.
"It rather gives the incentive to look for a new striker after the next season or in the next season who can then replace Lewy. That is then the job we have to do.
"There is little room for sadness, but you have to try to make the best out of the situation for the future."
Reflecting on his first season as Bayern coach, in which he led the Bavarian side to a 10th straight Bundesliga title but failed to get past the quarter-finals in the UEFA Champions League, Nagelsmann said: "It was tough. It was not that easy this season.
"The first half of the season was good. We expected another result in the cup, but in the end, we were very good in the [UEFA] Champions League group stage, and we were very good in the league.
"In the second part of the season, we were struggling a little bit. It was not that stable anymore. Sometimes we played well, we did not get the best results, especially in the [UEFA] Champions League. At the end, I think we could have done it a bit better."