"This is a critically important program that has [had] its problems in the past," Cook said. "We are confident in the capabilities of the F-35."
President-elect Donald Trump has been sharply critical of the costs of the F-35 program in recent tweets, and has stated that he has asked Boeing to price out an upgraded F-18 Super-Hornet jet that could replace the F-35 in critical roles for the US Navy.
The program is now projected to cost $400 billion for 2,457 jets, making it nearly $200 billion over budget though estimates of the eventual total cost have run as high as $1.5 trillion. The aircraft has already had problems with its software, cannon, ejection seat, helmet and other key components.
"This is an aircraft that the services are counting on not just the US but other countries as well," he added.
Israel received its first two F-35 jets on Monday.