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Ms Sereno last year expressed concerns over the names of judges Mr Duterte had in his list of purported drug suspects.
“Our judges may have been rendered vulnerable and veritable targets for any of those persons and groups who may consider judges as acceptable collateral damage in the war on drugs,” she said in a letter to Mr Duterte.
In January, she said unsolved killings of drug suspects has been eroding public trust in the country's criminal justice system.
"Despite all of these positive gains and even greater potential gains, we have to face the reality of the daily accounts of unsolved killings, many of them committed brazenly, with the public warnings against drug pushing or addiction," Ms Sereno said in a speech before business executives.
"It is not surprising therefore that the perception of the rule of law in our country has swung from marked improvement to a downgrade," she added.
Police say 3,200 suspects have been killed so far in shootouts during drug raids since Mr Duterte took office in June last year. But human rights activists insist the number is closer to 13,000. Two-thirds are believed to have been killed by paid assassins backed by police.
Ms Sereno has also been critical of Mr Duterte’s decision to impose martial rule over all of southern Mindanao island, after Muslim militants stormed Marawi city in May.
She said Mr Duterte should not have taken it upon himself to declare martial law. She had wanted to limit the scope of martial rule to only three provinces in Mindanao where Islamist extremists are known to thrive.
Ms Sereno is an appointee of former president Benigno Aquino.
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