The board of Johnston Press was paid nearly £2.3m in salary and benefits last year.
Chief executive Ashley Highfield, whose first year in charge has seen the company slash a quarter of its workforce, received £701,000 including a basic salary of £400,000. His total remuneration also included a performance-related bonus of £190,000.
Meanwhile, chief operating officer Danny Cammiade, who is due to step down at the end of March, was paid £825,000. His basic salary was £324,000, on top of which he received a cash bonus which, at £404,000, was 125 per cent of his salary.
The news follows Tuesday's announcement that, in addition to 1,300 job losses in 2012, up to 30 editorial posts are expected to be lost at the Scotsman, Scotland on Sunday, and Edinburgh Evening News. Scottish culture secretary Fiona Hyslop described the announcement as "extremely disappointing".
The company's annual report shows that the £2.284m paid to board members was slightly less than in 2011, when total remuneration was £2.517m. The reduction comes after a year when operating profits fell 12 per cent to £57m.
Chief financial officer Grant Murray has been paid £270,000 since his appointment in March 2011. Chairman Ian Russell's pay remained static from 2011 to 2012, at £130,000. Non-executive directors' pay was also frozen.
Danny Cammiade's resignation at the end of March will bring a close to his 21 years at the company, including eight years as chief operating officer since 2005.