Ackman said he was "wrong to indict an entire company."
"You don't call a company a sewer because a company made a mistake," Ackman told CNBC's "Fast Money: Halftime Report."
The drugmaker's shares had lost about 9 percent Monday but recovered half of the losses as Ackman spoke. Its shares have plunged about 70 percent this year, hitting Ackman, who owned about 9 percent of outstanding shares as of March 24.
Buffett, the chairman and CEO of Berkshire, took aim at Valeant earlier on Monday.
"I don't think you'd want your son to grow up and run a company in the manner that Valeant was run," Buffett told CNBC's "Squawk Box."
Ackman said he had "a lot of respect" for Buffett, but disagreed with his assessment of Valeant.
Ackman contended the drugmaker has made "appropriate changes in personnel." During a Senate hearing last week on Valeant's drug pricing, Ackman said his first priority was to make sure the company did not go bankrupt.
The company took a step toward that goal when it filed a delayed annual report on Friday.
Ackman also addressed Coca-Cola, the soft drink maker that major shareholder Berkshire Hathaway has vigorously defended. Ackman previously bashed the company for what he called marketing unhealthy products to children, and Munger responded to him and other critics Saturday.
"It's immature and stupid," he said of people who talked about Coke's defects without discussing its advantages.
Ackman reiterated his criticism of the company, saying "unfortunately Coca-Cola markets a product that causes harm."