The man was swiftly arrested but a spokeswoman said he was released later on the same day.
The man, who is known to police, will appear in Auckland District Court next week charged with assault with a weapon.
A Ministry of Justice spokeswoman said Judge Kiernan, who has nearly 15 years' experience on the bench, was unharmed by the attack.
She did not want to comment on the incident but it was confirmed yesterday that she took no time off work.
The poo thrower was not scheduled to appear in court on the day but it can be revealed he and the judge have history.
Just over a year ago she found the octogenarian guilty of assaulting a prominent New Zealander.
Judge Kiernan fined him $400 and ordered him to pay court costs of $130.
It is unclear yet as to whether he will appear before her or a different judge next week.
Ministry of Justice acting director of technical and judicial security Rick McKee said the department had invested heavily to improve court safety.
"We've introduced enhanced security measures, including employing additional court security officers, buying additional x-ray and metal detectors, and carrying more screening in more courts," he said.
"However, this was a serious incident and the ministry will be undertaking a review of it to see if any improvements could have been made."
Auckland District Court was the scene of another bizarre incident in September 2014.
Christopher O'Loughlin, 29, a man with a "massive history of previous convictions", added one of assault to the list when he hurled his jandal at Judge David Wilson, QC.
The incident was referred to by the victim in emails as "the case of the Jandal which missed".
For that and other offending, O'Loughlin was jailed for 10 months.
