Apple Inc. COO Timothy Cook received total compensation of $59.1 million in fiscal 2010 because of bonuses for running day-to-day operations during CEO Steve Jobs’s medical leave.

Cook was given a $5 million bonus and $52.3 million in stock awards for the year ended September 2010, Cupertino, Calif.-based Apple said yesterday in a regulatory filing. Cook’s total compensation was up from $1.64 million in 2009, while his salary remained at about $800,000.

Cook, 50, took over daily management when Jobs went on a nearly six-month medical leave to have a liver transplant in 2009. Jobs collected $1 last year, his salary since returning to Apple in 1997. He holds about 5.5 million shares and hasn’t sold any since rejoining Apple.

Apple rose $2.39 to $336.12.

Apple said yesterday that its annual meeting will take place Feb. 23, when a vote will be held on a shareholder proposal advocating for a public CEO succession plan.

Apple is recommending investors vote against the proposal, arguing that a public succession plan would reveal confidential business strategies to competitors and make it easier for them to lure away talented executives.