The visit included formal events with the Filipino President Rodrigo Roa Duterte and meetings with technical experts in areas that included rice production.
O'Neill said the countries "share a very warm history" that continued to grow as greater technical and cultural exchange took place.
"Engagement between Papua New Guinea and the Philippines go back to the 1800s when Filipino missionaries accompanied European Catholic priests to live with our people," O'Neill said upon arrival in Manila.
"As nation-states, we have had diplomatic relations for 43 years, and it is important that we continue to strengthen our engagement.
"Today, there are more than 35,000 Filipinos living in our country, making them largest group of expatriates in Papua New Guinea.
"Many Filipinos provide services in sectors that include healthcare and education, as well as working in many businesses."
The Prime Minister said he looked forward to expanding opportunities for bilateral engagement in agriculture.
"One of the most important elements in this visit will be to discuss opportunities for technical support from the Philippines to grow rice in Papua New Guinea.
"The Philippines is a world leader in rice cultivation, and they are interested to work with Papua New Guinea to expand our production.
"In rice trials conducted by Philippines agricultural experts, they have found our soil can yield double the rice per hectare than is possible in many countries in south-east Asia.
"This is because our soil is extremely fertile and for the most part has never been used for commercial agriculture or been exposed to pesticides."