Mr Farley was paid $1.2 million, including bonuses, in the 12 months to December 31, up from $931,950 in the prior year, the company's annual report says.
But non-executive director Donald McGauchie received a total of $206,380, up just $65 on the previous year.
The Australian Agricultural Company (AACo) made an $8.4 million loss in 2012 due to the suspension of controversial live cattle exports, which caused a $41 million writedown in the value of its properties in northern Australia.
Mr Farley in the report said the company's business model had been transformed and the operational results achieved over the past three years had been significant.
"With global food production expected to more than double by 2050, driven largely by the rising affluence of Asia's middle class, Australia's agriculture industry is on the doorstep of unprecedented opportunities to become a food bowl to these massive emerging economies," Mr Farley said.
He said the company was focused on continuing to drive improvements in the areas it could control and by managing its risk.
Shares in the company closed four cents higher at $1.31.