The disclosure, in an on Wednesday, comes a little over a week after Jobs revealed that his weight loss over the past year has been caused by a hormone imbalance.
"Unfortunately, the curiosity over my personal health continues to be a distraction not only for me and my family, but everyone else at Apple as well. In addition, during the past week I have learned that my health-related issues are more complex than I originally thought," Jobs wrote.
"In order to take myself out of the limelight and focus on my health ... I have decided to take a medical leave of absence until the end of June," he wrote.
Tim Cook, Apple's chief operating officer, will take over Apple's day-to-day operations during Jobs' absence. As COO he is responsible for Apple's worldwide sales and operations, and also heads the company's Macintosh division.
Jobs will remain CEO during his absence and be involved in major strategic decisions, said Apple spokeswoman Katie Cotton.
She declined to elaborate on Jobs' condition beyond what the statement says, including whether a hormone imbalance is still thought to be the cause of his weight loss.
Speculation about Jobs' health has dogged him since Apple's Worldwide Developer Conference in June, when many people thought he appeared gaunt. Earlier, in 2004, Jobs revealed he had undergone surgery for pancreatic cancer. When he took time off for surgery to remove that tumor, he also handed over the reins to Cook.
Earlier this month, amid rumors that he may once again be seriously ill, Jobs issued a on Jan. 5 in which he said doctors thought they had found the cause of his weight loss -- "a hormone imbalance that has been 'robbing' me of the proteins my body needs to be healthy. Sophisticated blood tests have confirmed this diagnosis."
Apple's share price tends to rise and fall on speculation about Jobs' health. While many companies have charismatic leaders, Jobs is thought to control even minor decisions at Apple, the company he cofounded in the 1970s and brought back to life after returning to it in the mid-1990s.
Following Wednesday's announcement, Apple's shares were trading about $5.45 lower in the after-hours markets, hovering at around $80 per share.
"Steve Jobs is more critical to Apple's operations than most CEOs are. Arguably he embodies Apple. He is Apple," said Roger Kay, president of Endpoint Technologies Associates.
In addition to his value as an innovator and a "tremendous motivator," Jobs' skills at negotiating with companies have been invaluable for Apple in the past few years, said Andy Hargreaves, an analyst with Pacific Crest Securities.
"Convincing a company like AT&T to partner with Apple on a product unseen, convincing the music industry that this is the wave of the future and they have to get on board" were both significant accomplishments, he said.
The drop in share price will be muted because rumors about Jobs' health have been circulating for months, Hargreaves said. "I think anyone that's been buying the stock in the last couple of months has been keenly aware that his health is an issue," he said.
Cook is thought to be a good choice to run the company during Jobs' absence, although he's not the person who will develop Apple's next iconic product.
"Tim Cook's the guy who makes the trains run on time. He's not the creative genius," Kay said. "Even though in some sense he is an excellent manager and is the backstop for Steve ... that's not going to do anything except make the trains run on time. That's not going to decide what the train should look like in five years."
Still, Jobs' absence is unlikely to affect short-term product plans, which will already have been decided, Kay noted.
(Agam Shah and James Niccolai in San Francisco contributed to this report.)