The Finance Ministry said neither minister Lim Guan Eng nor Prime Minister Dr Mahathir Mohamad were involved in the move to appoint Petron as a government fuel provider.
The ministry said this was an administrative decision on operative management, and as such the matter "was never referred to the prime minister nor the finance minister, and was done without political interference."
It added that Petron had also been negotiating the deal with the government since 2016 during the tenure of former prime minister Najib Abdul Razak – who has criticised Pakatan Harapan for Petron's appointment.
"Petron had made its application in 2016, and on Dec 2017 the company agreed to give the government small savings through its indent card programme.
"The negotiations began under the leadership of Najib, which shows that the previous government had no objections to consider Petron's application and the new federal government is only continuing the internal process through the existing guidelines," the ministry said in a statement today.
Najib had on Friday said the appointment of Petron created moral conflict for the Harapan government.
Petron's appointment had raised eyebrows as Mahathir's son Mirzan is a director in its parent company Petron Corporation, which is based in the Philippines.
Petron Malaysia, however, said Mirzan has no interest nor role in its local operations.
Meanwhile, the Finance Ministry said the appointment of Petron came at no cost to the government, and that it did not require his ministry's permission.
It also reiterated that other fuel companies such as BHP and Caltex were free to apply to enter the government's fuel provider panel.