Agricultural secretary Proceso Alcala said that the department has consulted exporters to find out which facilities have to be upgraded.
"It looks like the contamination (of exports) is coming from the packaging of small exporters so the best solution is for us to help them," Alcala added.
The agricultural department is providing around PHP500,000 ($11,476.3) to help small-scale operations. It is providing a total of PEP50m ($1.14m) for the project.
Recently, China has started inspecting all the shipments of fresh produce from the Philippines after scale insects were found in a shipment of Philippine bananas in March.
