The government has used the reset policy in the organic laws on constitutional organisations to undermine the National Human Rights Commission (NHRC) and the Election Commission (EC), say critics.
NHRC chairman What Tingsamitr said the set zero principles in the approved laws had ulterior motives behind them.
"The Constitutional Drafting Committee (CDC)'s explanation that the principle was created to improve standards of human rights is unreasonable," Mr What said on Friday at a seminar to mark the 17th anniversary of the NHRC.
Under the set zero principle, the six NHRC commissioners had to vacate their posts once the bill was enacted last December, and then assume a caretaker role until a new human rights body is appointed.
He said the NHRC has been praised by the international community, and under his tenure, it has already wrapped up 70% of complaints on rights violations.
If the current commissioners are allowed to continue in their posts, there will be less than 10% of cases left to be completed, he added.
Banjerd Singkaneti, dean of the Faculty of Law National Institute of Development Administration (Nida), said the set zero policy put those two independent agencies under the thumb of the CDC and National Legislative Assembly (NLA).
"If the organisation complies with the CDC and NLA, they will be allowed to stay. If not, they will be affected. Therefore, NHRC might not be able to work independently" he said.
Mr Banjerd added the set zero policy is double-standard because while the principle has been imposed on the NHRC and EC, it has not been applied to other constitutional organisations.
Mr Banjerd said that Section 25 of the charter is not conducive to human rights. The section says that the exercising of rights should not affect "national security" without giving a definition of "national security".
"National security may be interpreted as the government or the prime minister," he said.
In 2016, the Geneva-based National Human Rights Institutions downgraded the status of the Thai commission to "B", citing its politically-biased nature and unacceptably slow processes.