Francis Oppong, Cocobod's deputy chief executive for agronomy and quality control, said that farmers will also be given hybrid and drought-resistant varieties to improve bean quality.
Ghana, the world's second-largest cocoa producer behind Ivory Coast, launched the free seedlings scheme in 2011 in an effort to rehabilitate the crop. It has expanded the scheme steadily from 20 million seedlings in 2012 to 50 million this year.
The country's cocoa output topped a record 1 million tonnes in 2011 but has since remained at an average 800,000 tonnes.
Output for the 2014/15 season is running 23 percent below last year's because of erratic weather and poor agronomic practices, including inefficient disease control.
"Next year, we will significantly increase the amount (of seedlings) to farmers because we want to turn the crop around," Oppong told Reuters.
"It could be 60-70 million, or much more," he said, adding that Cocobod would announce details by the end of this year.
About 40 percent of Ghana's cocoa trees are old and must be replaced, Oppong said.
Cocobod also gave out free fertiliser to farmers last year.