A regulatory filing Thursday revealed Cook's salary rose to $1.4 million in 2012 from $900,000 but he received no stock awards this year, resulting in the much-smaller pay package, the Journal said.
Most of his compensation in 2011 came from a grant of shares awarded when he became chief executive, making him one of the highest paid chief executive officers, but Apple said he would not be getting any new shares.
"Mr. Cook's target cash compensation remains significantly below the median for CEOs of peer companies," Apple said in the filing.
His predecessor as head of Apple, Steve Jobs, famously took an annual salary of only $1.
Earlier this year, Apple's shares reached a high of $644, giving the company a market value of more than $600 billion and making it the world's most valuable firm.