Throughout the 1990s and early 2000s, Nayiri continued to serve in senior judicial capacities. At various points, he headed the Special Courts of Article 49, which dealt with confiscated property and assets, and later became the head of the Supreme Judicial Court of Judges. He was also a close advisor to the head of the Judiciary.
However, Nayiri’s legacy is anything but uncontroversial. International human rights organizations have consistently criticized his role in the 1988 executions. In 2019, Amnesty International explicitly named him among those responsible for what it described as “crimes against humanity.”
The report detailed how Nayiri and others conducted perfunctory interrogations of prisoners, many of whom were already serving long sentences, and ordered mass executions. “Take off your blindfold!” one former prisoner recalled being told. “When I took off my blindfold, I saw the committee in front of me and recognized Nayiri, Ishraqi, and Pourmohammadi.”