Move follows publication of leaked document warning Malaysia off oil drilling by Philippine media outlet.
The ministry said police would be informed and an internal investigation was under way, in a statement released late on Wednesday.
It did not name the outlet or confirm the authenticity of the note’s contents but did go into detail about Malaysia’s claims in the disputed South China Sea.
The Philippine Daily Inquirer reported on August 29 that China had sent the Malaysian embassy a diplomatic note to stop all oil exploration and drilling activities at Luconia Shoals, which lie about 100 kilometres off the Malaysian state of Sarawak.
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