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"It was a shock when I heard the news. I am disappointed and I hope there are no more such cases in future," Federer said at a sponsors meeting at Kilchberg near Zurich.
But Federer also noted that Agassi "has done a lot for tennis, both as a player and as a human being".
"Today, he raises millions of dollars for his foundation for disadvantaged children," the Swiss commented.
Agassi, one of just six men to have won all four Grand Slam titles and widely regarded as one of the sport's finest players, stunned tennis this week by revealing he'd taken the highly-addictive drug crystal methamphetamine in 1997.
The American, now 39, also admitted that he lied to the governing body of the ATP to escape a ban.
Federer noted that today, players must make themselves available for dope tests between 20 and 30 times a year.
"Our sport must stay clean," he stressed.
