The FCB coach revealed that he had some one-to-one time with the Polish striker before he netted against Fortuna Dusseldorf
Lewandowski netted a brace in Bayern’s 5-0 win and his double meant he has now recorded a goal against all 18 Bundesliga clubs.
Flick revealed how he had tried to inspire the striker, who moved onto 43 goals in all competitions this season.
“I told Robert Lewandowski that I was surprised to hear at the press conference that he had not yet scored a goal against Fortuna Dusseldorf and that he should change that as soon as possible,” he told a news conference.
“And of course he did.”
Bayern’s win saw them move 10 points clear at the top as they near an eighth straight league title, and they have netted 86 goals in 29 Bundesliga games this season.
But Flick insisted the 100-goal milestone was not a priority, with Bayern having five matches to net 14 times.
“There are other goals that are more important to me. That we have a very successful season,” he said.
“If this is the case, that we can score one or two goals more, that’s even better.
“But currently the focus is on the Bundesliga. To finish the league on the same pitch as we are now.”
Meanwhile, Lewandowski set another personal landmark as he grabbed his 42nd and 43rd goals of the season – meaning that he has now equalled his most prolific campaign to date.
The 31-year-old is also on 29 league goals and stands on the brink of hitting 30 in the Bundesliga for the third time, having reached that mark in 2015-16 and 2016-17.
His success this season has owed much to his stunning form in the Champions League, a competition in which he has already scored 11 times, despite playing only six matches.
Bayern are through to the last eight in Europe, though UEFA has yet to confirm any dates for the quarter-finals of the tournament, which they aim to conclude in August.