Fry, who took over as chief executive on 1 January last year, received a total remuneration of £959,000 in 2009 which included a salary of £525,000, cash and deferred share bonuses worth £420,000, with £14,000 of other benefits.
Over the same period Johnston Press, which publishes the Scotsman and Yorkshire Post, recorded a fall in pre-tax profits of 56 per cent to £43.3m as it wrote down the value of its newspaper titles and closed presses in Northern Ireland and Scotland.
Johnston Press was also forced to refinance is debt facility of £485m, in August, albeit at a greatly increased cost of borrowing. In addition, it cancelled the proposed sale of its Irish titles as it was unable to find a buyer willing to meet its valuation of the businesses.
Figures supplied in the group's annual report show that it also reduced headcount by 14 per cent to a total staff of 6,146 employees last year.
Chief financial officer Stuart Paterson took home £655,000 last year which included a salary of £361,000 and cash and share bonuses worth £292,000.
Despite his salary remaining the same Paterson's take home pay increased by 80 per cent as he had not been paid a bonus in 2008.
Danny Cammiade, Johnston Press chief operating officer, had a total remuneration of £590,000 last year. This included a salary of £324,000 and cash and share bonuses totalling £248,000.
Like Paterson, Cammiade saw his take home pay increase by 73 per cent, despite his basic salary being frozen, as he had not been paid a bonus the previous year.
Roger Parry, who stepped down as chairman of Johnston Press in April last year, was paid £43,000 by the company -- all as salary. His replacement Ian Russell was paid a salary of £114,000.
Union members across Johnston Press are expected to ballot later this month on a possible group-wide strike over the introduction of the controversial Atex content management technology and concerns about low staffing levels.
Oliver Luft writes for Press Gazette.