Growers from the South West province of the country, which is the world's third largest producer of cocoa, told Reuters they had been given only 40 per cent of the chemicals that were needed.
Most cocoa farmers depend on state funds or farming federations to supply them with pesticides but some communities have claimed they are not getting enough to ensure the crops are protected from potentially devastating diseases such as Black Pod and this will impact on productivity.
In addition, the South Western farmers said chemicals from a government-organised fund had not arrived in time for the start of the cocoa season in August.
Head of a local co-operative David Molonge Kinge told Reuters: "They told us there were stocks for us, but now we will get them for next season."
The cocoa plant is particularly susceptible to disease with the virulent fungus Black Pod responsible for the destruction of between 30 and 90 per cent of the bean each year.
The spread of Black Pod is usually contained by using copper-based fungicides and selectively pruning diseased pods but the effectiveness of the pesticide depends on climatic conditions in the crop area and, due to heavy rains, the amount of chemicals needed can vary.
Currently, 4 million metric tons of cocoa worth more than $4 billion (€3.1bn) are produced each year. The global chocolate market is worth $75 billion (€58.5bn) annually.
African cocoa producing countries, which include Cameroon, Cote d'Ivoire, Uganda and Ghana, account for around 80 per cent of global exports of the bean.