"For me what he does is a thousand times more important than what he says because what he does needs no interpretation," Klopp told reporters ahead of Saturday's first-round game against lower-tier SV Wilhelmshaven in the German Cup.
Lewandowski, whose contract runs out in 2014, had desperately wanted to move to treble winners Bayern but the club refused to sell him to their biggest league rivals, who have already poached the talented Mario Goetze from them.
On Wednesday, he told a Polish newspaper he felt betrayed by club officials - not Klopp - who had not honoured what the striker said was a verbal agreement to allow him to join Bayern.
"I was disappointed because people within the club said one thing to my face and then later it was different to what was agreed," the Poland international told Rzeczpospolita.
"When I myself promise something then I keep my word. I was always fair towards the club, I always give 100 percent."
Klopp said a meeting would be held with Lewandowski and his agent to clear the air.
"Whatever is left to be discussed will be discussed internally," he said. "The idea is to close this subject. Everything is in order. Nothing has changed since yesterday or the day before yesterday.
"I am convinced we will clear up everything in the coming days."
Lewandowski had a sensational run last season, scoring 24 league goals and adding another 10 in the Champions League, including four in one game against Real Madrid.
Earlier this week, he pledged his commitment to Dortmund saying whatever happened would not affect his performance.
The 24-year-old has already bagged his first silverware of the season, with Dortmund winning the German Super Cup by beating Bayern 4-2 last week.
Dortmund, who lost out to Bayern in all three competitions last season, will not receive a transfer fee if Lewandowski leaves as a free agent after his deal expires next year.