"It is with regret that I announce my resignation as Minister of State in the O'Neill Abel government," Marape said in a statement, referring to Deputy Prime Minister Charles Abel.
France's Total and its partners signed a long-awaited deal with Papua New Guinea on Tuesday that will allow initial work to start on a $13 billion plan to double the country's liquefied natural gas exports.
Developing the Pacific island nation's gas reserves is crucial for an economy that relies on LNG as its biggest export earner at a time when demand for the fuel is surging globally.
O'Neill's office said he accepted the resignation of Marape, who will remain a member of parliament.