"He is only doing harm to tennis," Becker told the website of the Sport Bild weekly on Tuesday. "I am asking myself 'why is he making this confession?'
"You could forget about it if he had had too many beers or smoked a joint. But we are talking about one of the worst drugs: crystal meth is a synthetic stimulant and one of the most dangerous drugs."
"I feel disappointed as an athlete. He has won many Grand Slams, some of them against me. If he won those because he was on speed it's simply unfair," said Becker.
Agassi, 39, revealed in his new autobiography he took crystal methamphetamine but escaped sanctions by lying to the men's tennis body ATP, saying he had accidentally taken a drink spiked by a former assistant.
Becker was not amused: "He sent a letter to the ATP that it wasn't deliberately. And then they, whoever was responsible there, turned a blind eye. That should not happen on either side."
Becker lost 10 of 14 duels with Agassi during his career, with no love lost between the two.
Several other players like the world leading duo of Roger Federer and Rafael Nadal have also expressed concern.
"It was a shock when I heard the news. I'm disappointed and I hope there are no more such cases in future. The sport must stay clean," said Federer last week.
Nadal said: "Why is he saying this now that he has retired? It damages the sport, it makes no sense. I'm the first one who wants to make sure tennis is clean."