Aquino said on Monday morning that their families had been estranged politically since 1967 but "his generation" in the Cojuangco clan had never "taken personally" their political differences.
He also cast doubts on suggestions that Cojuangco might have been behind his father's assassination.
"In truth, for us in Tarlac, in our generation, we did not take (our political differences) personally and I think we can say that we helped each other for the betterment of Tarlac," Aquino said in an interview with GMA Channel 7's Unang Hirit.
"So, are we now OK? We are no longer enemies. I think that's the closest thing that I could say today," he added.
While Cojuangco has been tightlipped over who was his bet in the presidential race, his daughter and brother Henry have come out in support of Aquino.
Danding Cojuangco was among the closest business associates of the dictator Ferdinand Marcos. Cojuangco, chairman of the San Miguel Corp., who was said to have used the coconut levy funds paid for by farmers to consolidate his interests in the SMC, was called the top Marcos crony due to his closeness to the Marcos regime.
He is cousin to the late former president Corazon C. Aquino, who was catapulted to power via the 1986 Edsa Revolution that toppled Marcos and exiled him to Hawaii. Cojuangco fled the country together with Marcos.
He returned to the country in the early 1990s and later regained control of the San Miguel Corp.
The issue of the coconut levy funds is still pending with the courts.
