Bilateral tensions have risen recently over naval disputes in contested areas of the South China Sea and the increasing U.S. military presence in the Philippines.
"Both sides reaffirmed the importance of properly managing differences through friendly consultations, as well as maintaining the general direction of Sino-Philippine friendship," Beijing's ministry said in a statement.
It came after Chinese Vice Foreign Minister began a three-day visit to Manila by meeting with Philippines counterpart Theresa Lazaro.
The talks also touched on aspects where both sides could work more closely, it said, yielding an agreement to deepen cooperation in agriculture, infrastructure, energy and culture.
Lazaro said in a statement that almost four years had passed since the last high-level diplomatic consultations between Beijing and Manila and that they should be held more often.
The Philippines earlier this week announced four new military bases under a defense agreement with the United States that would beef up Washington's military presence in the Southeast Asian country.
The bases in question would be located in various areas of the Philippines, including in a province facing the South China Sea. Some leaders of local governments at the sites opposed Manila's decision, worried they would be dragged into a conflict if one arose between the U.S. and China over Taiwan.
China's foreign ministry on Wednesday reiterated a warning to regional countries to be "vigilant" and avoid being used by the United States.