The lawyer travelled to The Hague to hand over his complaint in person to the office of ICC prosecutor.
Lawyer Jude Sabio urged the prosecutor at the International Criminal Court in The Hague to investigate Duterte and senior adminstration officials and bring charges of crimes against humanity against them for "the terrifying and gruesome situation of continuing mass murder in the Philippines".
Sabio, who is the lawyer for Duterte's confessed hitman Edgar Matobato, said the president "began his strategy or system of eliminating or killing persons suspected of crimes, including drug addicts and pushers" when he became mayor of Davao City in 1988.
"The 'repeated, unchanging and continuous' mass murder being conducted by the President Duterte has already resulted into the deaths of not less than 1,400 individuals in Davao City under his Davao Death Squad and not less than 7,000 individuals in his war on drugs at the national level," the filing said.
Sabio travelled to The Hague to hand over his complaint in person to the office of ICC prosecutor Fatou Bensouda.
There was no immediate reply from her office to an AFP request for comment, but Bensouda in October issued a strong statement about the alleged killings, warning those responsible could face prosecution.
"I am deeply concerned about these alleged killings and the fact that public statements from high officials of the... Philippines seem to condone such killings," she said.
"Let me be clear: any person in the Philippines who incites or engages in acts of mass violence including by ordering, requesting, encouraging or contributing... to the commission of crimes within the jurisdiction of the ICC is potentially liable for prosecution before the court."
Duterte won election by a landslide last May largely on his promise to launch a war on illegal drugs.
Although the campaign has proved popular at home, the president has faced international criticism for the thousands of alleged extrajudicial killings.
The government denies the allegations, and presidential spokesman Ernie Abella said Monday that police were already probing those suspected "of violating procedures."
He also pointed to an investigation by the country's Senate, in which Matobato was a star witness, and said the ICC "as a court of last resort, will only exercise jurisdiction over a case once legal remedies in the Philippines have been exhausted."
"The so-called 'extrajudicial killings', are not state-sanctioned or state-sponsored. Police authorities are conducting legitimate operations that require observance of operational protocols," Abella added.
Since it began work in 2002, the ICC says the prosecutor's office has received some 10,000 requests from individuals, groups or countries to investigate alleged crimes.
It is then up to the prosecutor to decide if there is enough cause to open a preliminary inquiry into whether a full-blown investigation is then merited. There are currently 10 preliminary examinations, and 10 full investigations under way.
A total of 23 cases have been dealt with, securing nine convictions and one acquittal. Five trials are ongoing.