There were a record number of entrants for this year's four categories, with Mr Thomas winning the overall prize for his landmark reporting on the failings of the Queensland health system.
Both Mr Thomas and Professor Doherty called for a national consensus on health, and an end to political point-scoring and work on endemic structural problems for the benefit of patients and taxpayers alike.
The political outcome of the "Dr Death" scandal is still being felt, with Queensland Premier Peter Beattie recently announcing measures worth more than $6 billion to support the ailing health system. Many of the problems were brought to light by Mr Thomas' and the Courier Mail's extensive coverage.
Professor Peter Doherty told The National Press Club during a nationally televised address today that Australia's economic and scientific future lies in innovation, finding niche markets and fostering human capital to keep more talented Australians working in their homeland.
He also encouraged media outlets and his fellow scientists to work more closely together on promoting the value of Australian research, and its everyday value to Australians through work done in areas such as innovative medicines.
The chairman of Medicines Australia, John Young, in praising the award winners said for most Australians there was no more important subject than their health.
"Without your reporting, Australians would lack much of the essential information they need to understand issues impacting health care in this country better, whether it is from a political, financial, medical or community perspective," he said.
The full list of winners is:
Medicines Australia - Health Journalist of the Year
Winner - Hedley
Contact: Paul Chamberlin