Murray, ranked number two in the world behind Djokovic, has been outspoken on drug use in the sport in recent weeks and welcomed the ban imposed on Maria Sharapova following her failed test for meldonium at the Australian Open.
The Scot, who was beaten by Rafael Nadal in the Monte Carlo Masters semi-final on Saturday, has also talked of being suspicious of opponents who he thought were not getting tired in matches.
And Becker, a six-time grand slam winner, has accused Murray of being “out of order”.
Speaking at the Laureus World Sport Awards, the German told the Daily Mail: “We have random drug-testing and unless it’s proven, they are 100 per cent innocent.
“So to assume something because somebody has won a grand slam or is fitter is totally out of order. Andy is one of the fittest players on the tour – he often outlasts players and nobody is questioning his ethics.
The funniest thing about Becker slamming Murray is that he accused Muster of doping in 1996 and Muster's fitness coach is now Djokovic's.— Chris de Waard (@TennisPurist) April 17, 2016
“I believe 100 per cent Andy is clean. Roger (Federer) is clean, Rafa is clean, all these guys are clean. Novak gets tested a lot. That can mean twice in a grand slam.”
Murray had told the Mail On Sunday: “I have played against players and thought, ‘They won’t go away’ or ‘They don’t seem to be getting tired’.
“Have I ever been suspicious of someone? Yeah. You hear things. It’s harder to tell in our sport as people can make big improvements to a stroke or start serving better because they have made technical changes.
“If it’s purely physical and you’re watching someone playing six-hour matches over and over and showing no signs of being tired, you’d look at that.”