The two-time major winner said he had faced players and thought “they don’t seem to be getting tired”.
Becker, who coaches world number one Novak Djokovic, said: “Unless it’s proven, they are 100% innocent.”
“To assume something because somebody has won a Grand Slam or is fitter, is totally out of order.”
Murray made the comments in an interview with the Mail on Sunday.
Becker was speaking at the Laureus World Sports Awards, where he said: “I believe 100% Andy is clean.
“Roger [Federer] is clean, Rafa [Nadal] is clean, all these guys are clean. Novak gets tested a lot.”
So Becker is clearly unimpressed with Murray.
The German three-time Wimbledon winner was fined for suggesting a player was doping during his playing career.
In 1995, Becker lost the Monte Carlo Masters final to Thomas Muster in five sets, a day after the Austrian complained of dehydration in his semi-final.
Muster had even spent the night before the final on a drip in hospital, but won from two sets down, saving match points in the process.
Becker was fined for expressing his astonishment that his opponent had recovered so quickly, in remarks that were widely interpreted as implying Muster had taken illegal drugs.
Andy Murray has been a strong critic of Maria Sharapova after the Russian tested positive for meldonium at the Australian Open in January.
The five-time major winner blamed the use of the drug on a variety of physical ailments including a longstanding heart problem.
Murray welcomed her provisional ban, saying it showed tennis was not covering up for its “big stars”.
He has been a loud voice in the call for more money to be put towards the fight against doping in tennis.
Speaking at the Indian Wells Masters in March he said: “It’s better than it was a few years ago and last season I got tested loads.
“But this year I’ve been tested only twice so far, and we’re three months into the year, which is clearly not enough.”