Dr Boston, the outspoken QCA chief executive who embarked on a root-and-branch overhaul of the authority last year, may now be the highest-paid figure in education.
The Australian received pound;104,699 in benefits in 2003-4, including pound;26,985 in tax paid by the QCA, and free return flights to Sydney, arranged with the Government when he was recruited from the New South Wales education department in 2002.
Under the benefits package, he also had rent paid on a London property. His basic salary was pound;118,312, with a performance-related bonus adding a further pound;19,500.
Dr Boston, 61, appears to have been able to name his price as the Department for Education and Skills searched the world to fill the post, which was left vacant for nearly eight months following David Hargreaves's sudden retirement in 2001.
However, his basic salary is not the highest among QCA executives. Jonathan Ford, appointed last year to take charge of the "modernisation" of the exams system, received pound;128,750.
Dr Ford, head of the National Assessment Agency, a division of QCA, whose boss is Dr Boston, did not receive any bonus or benefits in 2003-4, the accounts show. The financial statements for the year ending March 31 also reveal that the QCA spent pound;2.6 million on redundancy costs last year, following the radical restructuring instigated by Dr Boston.
Having arrived in the midst of the A-level regrading crisis of 2002, Dr Boston made senior staff reapply for their jobs, and the authority's workforce was cut from 603 to 570. The job losses included at least 16 senior managers. Dr Boston then appointed several newcomers from outside education to top posts. Their bonuses, listed for the first time in the accounts, dwarf those paid out in recent years.
Total bonuses for 2003-4 were pound;84,150, compared to pound;17,871 last year and only pound;8,545 in 2000-01. Basic pay was at least in line with what senior executives were paid in the past.
Supporters of Dr Boston and his reforms will argue that the money has been well spent, with the QCA having escaped any major problems since the debacle of 2002, the biggest crisis in its history.
Dean Rogers, national officer for the Public and Commercial Services union, said that the changes made QCA executives' salary packages "more competitive" with those within organisations such as the Office for Standards in Education, and secondary headteachers.
He said that the importance of the work of all those at the QCA should be recognised by the Treasury, which is proposing thousands of job cuts across the public services.
A TES survey last year identified Mark Haysom, chief executive of the Learning and Skills Council, as the highest-earning person in education, on a pound;180,000 basic salary, thought to equate to pound;200,000 with benefits.
The QCA had a total gross income of pound;92.3m in 2003-4. Of this, pound;35.5m was spent on national curriculum tests, a 48 per cent increase on the pound;24m spent in 2000.