Nicola Sturgeon says the money given to already highly-paid doctors should be redistributed to a wider range of health workers.
She has urged Ron Amy, chairman of the Doctors' and Dentists' Review Body (DDRB), to freeze distinction awards at 2009/10 levels and not to increase the number of awards.
Distinction and clinical excellence awards are paid to academic GPs and consultants for outstanding professional work. They can be worth between £35,484 and £75,889 a year on top of salaries.
Ms Sturgeon said: ‘The existing schemes are outdated and do little to create a drive for excellence throughout the clinical teams we have now.'
60 academic GPs enjoy national excellence awards, including two at the highest (platinum) level: Martin Roland, professor of health services research at Cambridge and Professor Roger Jones, head of general practice at King's College, London.
Other GPs do not qualify for distinction awards. They get seniority pay instead, escalating with years of experience.
In letters to prime minister Gordon Brown and the health secretaries of England, Wales and Northern Ireland, Ms Sturgeon has called for UK-wide backing to ensure no constituent countries lose their competitive advantage.
Ms Sturgeon's New Year's drive follows a campaign by RCN Scotland for all NHS staff to be rewarded in a similar way to consultants.
Almost 12% of consultants received a distinction or clinical excellence award in 2009.