Judicial players say the magistrate’s arrest went against a court order and are seeking to stop Haji from charging him.
A Nairobi court on Tuesday released Mr Kagoni on Sh200,000 cash bail.
But Chief Magistrate Lucas Onyina left his three co-accused in custody as they waited to take their pleas.
The embarrassing episode on the prosecution of Mombasa Principal Magistrate Edgar Kagoni, who is accused of helping in the disappearance of exhibits worth Sh30 million in a narcotics case, has once again sparked a war between the Directorate of Public Prosecutions (DPP) and the Judiciary.
The DPP and the Judiciary are part of the same system and a good working relationship between them is critical for the dispensation of justice. But DPP Noordin Haji is learning from experience that prosecuting a judge or a magistrate is a tall order.
A Nairobi court on Tuesday released Mr Kagoni on Sh200,000 cash bail. But Chief Magistrate Lucas Onyina left his three co-accused in custody as they waited to take their pleas.
Meanwhile, the fact that the magistrate was held the previous night despite the orders of the High Court in Mombasa against such a move has not gone unnoticed.
The DPP was not available for comment as he was said to be out of the country on official business.
But other judicial players have warned that by refusing to release the magistrate after a Mombasa court temporarily stopped the bid to charge Mr Kagoni, the DPP risks reigniting his icy relationship with the Judiciary while in the middle of a spirited war against graft.
The Law Society of Kenya (LSK) last evening termed the DPP’s move to charge Mr Kagoni as unconstitutional.
“It is vital in a democracy that individual judicial officers and the Judiciary as a whole be impartial and independent of any external pressures so that those who appear before them and the wider public can have confidence that their cases will be decided fairly and in accordance with the law,” LSK President Allen Gichuhi said.
“It therefore follows that judicial officers must be adequately safeguarded and only subjected to constitutionally prescribed disciplinary mechanisms not undermined and intimidated by fellow players in the criminal justice sector in full glare of the public,” he added.
In their appeal against the decision to charge Mr Kagoni, his lawyers, led by Mr Nelson Havi and Mr Vincent Omollo, argued that the independence of the judicial officer is guaranteed by the Constitution.
“The intended prosecution of the petitioner in respect of a matter he handled as a judicial officer is a violation of the Constitution,” Mr Havi said.
The Kenya Magistrates and Judges Association (KMJA), which also filed a suit defending Mr Kagoni, argued that the DPP intended to intimidate members of the Judiciary, and that there was no legal or factual justification for charging Mr Kagoni with theft of exhibits.
“The DPP seems keen on punishing Mr Kagoni for previously disallowing an application made on behalf of the republic, thus the decision is made in bad faith and in brazen violation of public interest and the magistrate’s exercise of authority done in lawful performance of judicial function,” KMJA said.
The argument is similar to that Deputy Chief Justice Philomena Mwilu’s lawyers used when fighting a move by the DPP to charge her. They argued that the criminal prosecution of a sitting Supreme Court judge amounted to a violation of the independence of the Judiciary.
Eventually, the case was thrown out on a technicality because of the way the Directorate of Criminal Investigations (DCI) had collected information against Justice Mwilu.
The new tension between the DPP and Judiciary is coming seven months after Mr Hajji and Chief Justice David Maraga agreed to stop blame games between their departments and close ranks to fight graft. They agreed that corruption cases should, at most, take five months, which is still proving a tall order.
Despite the truce, the DPP has recently been hit by a string of adversarial court decisions. This has exposed the uphill task Mr Haji faces as he strives to get his first big conviction in the more than 1,000 cases he has filed since taking over in March last year.
On Wednesday, for instance, Nairobi Chief Magistrate Martha Mutuku threw out a request by the DPP to introduce four more witnesses at the tail end of an Anglo Leasing case.
In addition, the DPP is waiting for the hearing of an appeal he filed together with the Ethics and Anti-Corruption Commission challenging a ruling last month that outlawed the use of secret search warrants during investigations.
The move could undermine 1,036 corruption cases, they said.