Eng Aik Meng will leave the company on Sep 1 to take a new position outside the transportation industry, NOL said in a statement.
Kenneth Glenn, an industry veteran and current company head of the North Asia region, will replace him.
In his new role, Mr Glenn will manage APL's global container transportation business, which includes shipping and rail operations. He will also be responsible for the company's marine terminals in the US, Asia and Europe.
NOL said in April that its CEO Ron Widdows will retire by the end of 2011. He will be replaced by Ng Yat Chung, a senior executive from state investor Temasek Holdings.