The senate joint inquiry, brought by the the committee on Justice and Human Rights and the Committee on Public Order and Dangerous Drugs, will examine testimony from both the families of those killed -- many by police -- and also from ranking officials.
Duterte has repeatedly said that the killings of drug suspects are lawful if police are acting in self defense.
One relative, the pregnant live-in partner of a victim of the war on drugs, JP Bertes, testified before the hearing. Both Bertes and his father-in-law were allegedly killed by police in Pasay City, Metro Manila, on July 6.
She admits her husband sold drugs. He had been arrested in 2015 but, she says, was released after paying crooked cops a bribe. Last month, however, she said policemen picked up the two men before killing them.
The woman told the joint inquiry a total of nine policemen arrested her partner and his father, Renato, at the family home, despite the lack of an arrest warrant.
One policeman even took off the underwear of her two-year-old daughter and did an anal search, which traumatized her child, she testified. She later filed a complaint with the Department of Social Welfare over the alleged molestation.
She said the two men were beaten up and brought to the local police station, and later shot and killed at another police anti-drugs facility.
Pasay City chief Police investigator Nolasco Bathan told the inquiry two of the policemen have been charged with murder, only this morning, before the hearing.
A local commission on human rights investigation said they found evidence of torture and "arbitrary deprivation of life."
The witness said that her common-law husband and father-in-law were not bad people and did not deserve their fate.
"Drug addicts are not bad people, they can still change," she said.
War of drugs out of control?
The war on drugs has widespread support in the country, with Duterte enjoying a 91% approval rating at the end of July, largely on the back of his hard line on drug crime.
However, the policies are not without their critics and this weeks hearings were convened by Senator Leila De Lima, one of the president's most outspoken critics.
De Lima said she would put aside her war of words with Duterte
to ensure the probe into the extrajudicial killings unleashed by the campaign on drugs will be conducted "in the most professional manner."
She claims the war, which has seen hundreds of deaths at police hands, is a "very important issue of public interest." saying that even the international community has taken notice of "this phenomenon of summary executions."
The country's top police officer, Philippines National Police (PNP) chief Ronald Dela Rosa reported in testimony that 712 suspects have been killed in police operations since the war on drugs began, and that internal police investigations in these cases are ongoing.
Hundreds of deaths
Dela Rosa was also grilled by Senator Antonio Trillanes about the police department's response to the 1,067 drug-related killings, many of which have been attributed to vigilantes, which have occurred since the beginning of July.
Dela Rosa said that the "cases are under investigation" and that he is encouraging officers to fast-track them. He insisted that the police were not involved in the deaths.
"We have nothing to do with the vigilante killings"
The nation's top officer, who was elevated to the role when his longtime friend, confidante and colleague Duterte was elected, testified that his officers had arrested 10,153 drug pushers and users since the war on drugs began at the beginning of June.
He added that more than 600,000 involved in illegal drugs had surrendered voluntarily, many as a result of "knock and plead" operations in local neighborhoods, where police invite suspected users to submit themselves to local authorities for registration.
In 6,000 police operations, 718 people have so far been killed, he said, and as a result of the raids drugs worth $51 million (2.38 billion pesos) have been seized. CNN could not independently verify the figures provided by the government.
The police does not and will not condone vigilante killings, he said asserting that these have been perpetrated by crime syndicates. "The police will ensure enforce the full force of the law against them," he told the hearing. "I hope this hearing will help bring a resolution to the drug problem."
"The PNP remains loyal to our mandate."
The hearings continue Tuesday.