Figures included in the annual report, released yesterday show the majority of the listed salaries ranged from $100,000 to about $150,000.
There were 82 employees in that bracket.
After the top salary, one person earned between $490,001 and $500,000 in the year ended September.
Retiring board chairman Eoin Garden was paid $139,993 in the year.
Total wages, salaries and benefits increased to $315.1 million from $290.2 million.
SFF said Mr Cooper's salary had been determined based on advice from an external consultant and had been set at the median of the market for the role.
It contained an at-risk element which was not paid unless certain criteria had been met.
Former chairman Owen Poole was paid $126,000.
Top-paid Alliance directors received $50,000 for their services while top-paid SFF directors received more than $62,000.
Alliance did not include its total employee remuneration in its annual report and said the figures included 15 employees made redundant during the year.
SFF reported a $36.5 million loss in the year, a reduction on the $42.2 million loss reported in the previous corresponding period (pcp).
The meat processing group received a tax refund of nearly $8 million to take the after-tax loss to $28.55 million, compared with a loss of $31.1 million in the pcp. In the 2012 financial year, the group received an $11 million tax refund.
SFF made gains on foreign exchange to help reduce the annual loss further to $27.8 million from $33 million previously.
Sales for the year were down slightly at $1.99 billion, from $2 billion. At the end of the period, the group had consolidated assets of $833.3 million, up from $828.5 million in the pcp.
Total current assets were down slightly at $403 million and total current liabilities were up more than $40 million to $502 million.
There was a substantial improvement in SFF's cash flows from operations which were -$5.07 million in the reported period compared with -$104 million in the pcp. A similar trend was noted for the Alliance Group.
The group's report showed China leapt ahead to be SFF's largest customer, with sales in the year of more than $332.4 million, compared with $190 million in 2012.
Previously, the United States had been the largest market, with sales of $292.6 million in 2012, slipping to second with sales of $263.9 million in 2013.
New Zealand sales also fell in the period to $228.9 million, from $282 million, but sales to both the United Kingdom and Australia increased.
Sales to Japan, Korea, Canada, Asia/the Middle East, Europe and the rest of the world were all down in the period.
Alliance made an operating profit in the year to September of $18.2 million, including restructuring expenses, compared with a loss of $54 million in the pcp.
The reported profit was $5.6 million, compared with a loss of $50.8 million.
The group paid $2.8 million in tax in 2013 and received a tax credit of $19.8 million in 2012.
Alliance had total assets of $485 million at balance date, down from $579.7 million. It had current assets of $236.3 million and total current liabilities of $66.9 million at balance date. Net cash flow from operating activities was $89 million compared with -$163 million in the previous period.
