"Mr. Cook recognizes imputed taxable income and is not provided a tax reimbursement for personal use of private aircraft", Apple said in its filing.
Cook's actual salary saw a comparatively smaller $57,692 increase, but the bulk of his nearly $4 million raise came from performance-based cash bonuses.
As a result of the satisfactory sales and profit in 2017, Apple is increasing Tim Cook's salary.
Cook's personal security costs also totalled $US224,216, ($A287,702) according to the filing.
As the head of the world's most valuable company, Mr Cook is also now forced to use private planes to travel for both business and personal purposes. Due to slumping iPhone sales in 2016, Cook's pay was cut 15%.
Apple's CEO since 2011 saw his salary rise to about $12.8 million in fiscal year 2017, which ended in September, from about $8.7 million in the prior fiscal year, according to a SEC filing from Apple on Wednesday. The flight policy was implemented in the interest of efficiency and security in 2017, based on the highly visible role as CEO of Cook.
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In addition, Apple expensed over $224,000 for incremental private costs for security for the CEO, says the proxy statement, including the hiring of personnel for the specific benefit of Cook.
The market capitalization for the iPhone maker has been hovering around $900 billion and is up almost 50 percent for the year.
Apple sold 78.29 million iPhones in the first quarter ended December 31, up from 74.78 million a year ago.
Apple introduced the iPhone X late this year, its most expensive smartphone since the iPhone 6.
Apple's executive compensation programme is created to reward its senior-level officials when the company does well, and dock them when it doesn't.