"A great number of state officials are implicated... from what I'm beginning to realise from reports, it must be thousands who were directly bribed from Switzerland," Stavros Kontonis told state agency ANA radio.
"National health service doctors and state officials were bribed to promote drugs in an illegal and anti-scientific manner," Kontonis said.
Scores of people have been questioned in a probe ongoing since last year, with anti-corruption prosecutors also visiting Novartis's premises near Athens earlier this year to gather evidence.
The case gained attention following a suicide attempt in Athens on New Year's Day, by a Novartis manager.
That attempt was thwarted by police and according to the judicial source, the manager was one of those questioned over alleged corruption.
Kontonis on Friday said Novartis continued to sell "overpriced" drugs even after the country was hit by economic crisis in 2010 and huge cuts were imposed on state budgets, leaving many Greeks without access to affordable medicine.
In January, Novartis issued a statement saying it was "aware of the media reports about our business practises" in Greece and that it was seeking more information and was cooperating with the authorities.
"Novartis is committed to the highest standards of ethical business conduct and regulatory compliance in all aspects of its work and takes any allegation of misconduct extremely seriously," the company said in the statement.
The Swiss pharmaceutical giant was investigated by US authorities in 2014, accused of paying bribes in order to boost sales of some of its medicines, and was later fined $390 million (366 million euros) by the US Justice Department.
In March, Novartis also paid $25 million (22.4 million euros) to settle claims involving its Chinese subsidiary.