Mr Phairoj was responding to a proposal by Pheu Thai Party list MP Watthana Muangsuk to jettison the Administrative Court and the Constitution Court as part of the government's constitutional amendment drive.
Mr Watthana said in an interview with Matichon newspaper earlier this week that the number of independent organisations should be kept to a minimum. He said the two courts were no longer required and they should be reduced to only divisions of the Supreme Court.
Mr Phairoj, however, said the Administrative Court was created under the 1997 constitution, marking a significant milestone in the country's administrative justice system.
The court has played a role in setting standards of administrative duties and public services by state agencies, Mr Phairoj said. He did not think the proposal to scrap the court could be deemed as a step forward.
Mr Phairoj dismissed Mr Watthana's claim the Administrative Court was handling only a small number of cases and should be scrapped.
He said the court, along with its regional branches, actually handles between 6,000 and 7,000 cases each year.
More than 70,000 cases have been filed with the court over the past 11 years.
Mr Phairoj said the court's role is authorised by the constitution to protect the public from abuse of authority by state agencies, not to interfere with the exercise of the executive power as alleged.
The court was always careful in issuing temporary junctions suspending state operations, to ensure its decision would not obstruct the administration of the country or affect the public as a whole, he said.
He also rejected claims the court's structure leaves it immune to scrutiny.
Even if the court enjoys independence in hearing cases, its structure allows members of a panel of judges to contest each other. There is also the commissaire du gouvernement to keep a balance at the Administrative Court, Mr Phairoj said.
He stressed the judiciary's independence is significant and steps must be taken to ensure the judicial bodies are not meddled with.
Deputy court spokeswoman Saithip Sukkhathiphan said the Administrative Court helps ordinary people who are powerless against the state.
"The court's judges are not above the law. They can be scrutinised, and impeached by the National Anti-Corruption Commission. They also come under the Criminal Code covering the duties of judges," Ms Saithip said.
However, Mr Watthana told a parliamentary committee vetting the charter legislation, which held its first meeting yesterday, that he did not propose abolishing independent bodies and the two courts.
He merely suggested the courts and independent bodies should assume their authority rightfully and transparently and they should distance themselves from any stakeholders.