Figures show that GPs contracted to provide services to the NHS saw their average income before tax stand at £88,800 in 2012-13, up £100 on the previous year but down from £90,619 in 2005-6.
Across the UK as a whole, average income for GPs fell from a peak of £110,000 in 2005-6 to £102,000 in 2012-13.
The British Medical Association (BMA) Scotland said while general practice had seen increased investment in recent years, it had not kept up with inflation and other extra demands placed on GPs.
The Scottish Government said it had invested more in general practice in recent years as well as giving doctors recommended rises in pay.
The latest figures, published by the Health and Social Care Information Centre (HSCIC) also revealed pay for GPs in Scotland continued to lag behind other parts of the UK.
While average pay for self-employed contractor GPs, who make up the bulk of GPs in Scotland, stood at £88,800 in 2012-13, this compared with pay in England standing at £105,100, in Northern Ireland at £92,200 and in Wales at £91,000.
A salaried GP in Scotland, employed on a fixed wage, earned an average of £54,200, compared with £56,600 in England. Scottish GPs were also less likely to earn the highest rates of pay.
The HSCIC figures showed that 420 GPs in Scotland earned more than £125,000 before tax – 11.2 per cent of all GPs. But in England 27.5 per cent of GPs earned above this level.
The largest proportion of GPs in Scotland earned between £75,000 and £100,000, at 33.6 per cent.
Out of the total funding given to GP practices, doctors must pay for expenses such as the cost of employing other practice staff, their premises and other bills before they take their own income. Last year, the biggest expense was employee costs.
Other figures out yesterday also showed a fall in pay for dentists employed to provide services for the NHS. In Scotland self-employed dentists earned an average of £68,800 in 2012-13, compared with £71,700 in 2011-12 – a 4 per cent decrease.
HSCIC chairman Kingsley Manning said: “These reports provide further insight into the income of GPs and dentists that carry out NHS work in the UK.
“The data shows a gradual decline in average income of both GPs and dentists. Contractor GPs have seen an increase in their expenses, higher than the increase in their gross earnings, which has meant that their taxable income is less than last year.”
Dr Alan McDevitt, chairman of the BMA’s Scottish GPs committee, said: “GP earnings have fallen in recent years and although there has been an increase in investment in Scottish general practice, it has failed to keep pace with inflation, the growing population and the rise in demand for more complex care.
“GPs in Scotland continue to earn less than colleagues in any other part of the UK, which will do little to improve the recruitment crisis in the profession.”
A Scottish Government spokeswoman said: “This government is committed to continuing to support, build upon and sustain Scottish general practice. We recently negotiated a new contract with GPs that will give the profession financial and contractual stability until April 2017.
“We’ve also further reduced ‘quality and outcomes framework’ requirements, ensuring more of a GP’s income is paid through a core payment rather than performance-related pay. This also reduces the bureaucratic burden on general practice, freeing up GPs to spend more time with patients.
“For 2014-15 the Scottish Government has implemented the recommendations of the doctor and dentists’ pay review body in full, investing an additional £1.8 million into GP services.”