The policy was implemented this year "in the interests of security and efficiency based on our global profile and the highly visible nature of Mr. Cook's role as CEO."
The filing noted that the value of the private flights is calculated as "imputed taxable income" which is not reimbursed by Apple. So Cook pays tax on it.
It comes as Cook's yearly bonus was increased by 74 per cent as Apple reported higher revenue and profits.
In addition to his US$9.33 million ($13.1m) bonus, Cook receives a US$3.06m ($4.3m) salary and US$89.2m ($125.8m) in Apple stock, for a total of US$102m ($143.9m) this year alone.
Cook's personal security costs also totalled US$224,216, ($316,357) according to the filing.
Cook took home far less than other top Apple executives including chief financial officer Luca Maestri and senior vice president Angela Ahrendts, who received some US$24m ($33.8m) for the year.
The market capitalisation for the iPhone maker has been hovering around US$900 billion ($1.2 trillion) and is up nearly 50 per cent for the year.
Since Cook took over from Steve Jobs in 2011, the company's share price has risen more than 200 per cent and has accumulated a war chest of over US$250b ($352.7b) in cash, The New York Post also reports.
Apple's stock surged 37 per cent in fiscal 2017, more than doubling the increase in the S&P 500.
Apple introduced the iPhone X late this year, its most expensive smartphone since the iPhone 6.
But it appears that the iPhone X has hit a wall as company shares took a tumble and sales expectations were down.
Wall Street's main indices faced pressure this week following a 2.8 per cent drop in Apple's shares on a report of weak iPhone X demand.
Apple will slash its sales forecast for its flagship phone in the current quarter to 30 million units, down from what it said was an initial plan of 50 million units, Taiwan's Economic Daily reported, citing unidentified sources.
That, along with some bearish brokerage calls on iPhone X demand, put its shares on track for their worst single-day per centage fall since August 10.
Shares of companies that supply parts to Apple, including Broadcom, Skyworks Solutions, Finisar and Lumentum Holdings, also took a hit as they fell between 1.8 per cent and 3.5 per cent.
Apple is also facing competition from Samsung, which is recovering from the Galaxy Note 7's worldwide recall after fires. Chinese brands such as Huawei, Oppo and Xiaomi are also fighting for customers in China and other emerging markets, Bloomberg reports.
