Chief Justice Esther Hayut on Monday issued a warning to all judges, telling them to "watch your step."
The unusual message followed a Channel 10 News report on Sunday, exposing a string of text messages suggesting that the judge assigned to Case 4,000 and the lead attorney investigating the case for the Israel Securities Authority illicitly coordinated legal proceedings.
Tel Aviv Magistrates' Court Judge Ronit Poznanski-Katz and ISA attorney Eran Shaham-Shavit have both been removed from the case, which revolves around corruption allegations involving Prime Minister Benjamin Netanyahu and his close associates.
Justice Minister Ayelet Shaked and Hayut have asked the Judiciary Ombudsman's Office, headed by retired Supreme Court Justice Eliezer Rivlin, to investigate the incident.
In her letter to judges, Hayut wrote: "Unfortunately, the judiciary has found itself in the eye of the storm over an incident reported in the media about the conduct of a Tel Aviv Magistrates' Court judge presiding over the arraignment proceedings in Case 4,000.
"The justice minister and I have asked the Judiciary Ombudsman's Office to investigate the issue as soon as we learned of it from the media. The ombudsman was asked to deal with this issue urgently and I have no doubt he will do so. This is the course of action the justice minister and I can take under the law at this point.
"This morning, which is difficult for all of us, I would like to express my deep appreciation for your dedication and hard work. We, the judges and registrars, support each other in all our actions. Therefore, I urge you to watch your step, be careful in your words and in your conduct and above all, I urge you to keep your spirits up.
"We will continue to do our work professionally and faithfully and will continue to do everything in our power to preserve the public's faith in the legal system, which numbers over 700 judges and senior officials who give their all to this job year-round."
Lawmakers on Monday harshly criticized law enforcement officials over the affair, saying it cast doubt over the integrity of the legal proceedings as a whole.