The doctors' union has denied claims that its chairman and other senior figures have enjoyed salaries hikes of up to 137%.
The British Medical Association (BMA), which represents around 153,000 doctors in the UK, said a large portion of their pay is put back into the NHS as "compensation" to their employers for the time they are not practising medicine.
Dr Mark Porter, the elected BMA council chair, was reported to have seen his salary rise from £88,320 last year to £171,692 - an increase of 94%.
But a BMA spokesman said most of it is actually paid to University Hospitals Coventry and Warwickshire (UHCW) NHS Trust, where Dr Porter is a consultant anaesthetist, to reimburse it for all the time his union role means he is not there.
"The vast, vast majority of that money does not end up in Mark's pocket," the spokesman said.
"It ends up in the NHS as compensation for his time at the BMA."
Dr Philip Banfield, chairman of the BMA in Wales, received a salary increase of 99%, taking it up to £62,631 this year, according to figures published in the Guardian, while Dr John Woods, its chairman in Northern Ireland, is now on £62,631 - up 108%.
The paper said that Dr Peter Bennie, chairman in Scotland, saw his pay go up to £76,431, an increase of 137%.
The BMA spokesman said: "As the recognised leaders of their profession the BMA's chief officers are active, practising doctors.
"For some, holding such a position has become itself a full-time role. It is only right that these increasing demands are appropriately recognised.
"BMA Council and its remuneration committee made its decision in 2014 - without the input or even the presence of those officers affected. In most cases some of the financial package is paid to the doctors' employers in order to release them to attend work on behalf of the profession.
"If we are to have the right people in the job, it is vital that they are not discouraged from doing so because of financial penalties.
"The levels of pay were recommended by the BMA's Remuneration Committee, independent of the chief officers, with oversight from the BMA's audit committee and the oversight and finance committee."
The BMA later confirmed that £54,000 is deducted from Dr Porter's salary and paid to the NHS trust where he works, while he has chosen to relinquish £77,000, leaving him with a payment of £40,000.