Judge Colgan heard the case over three days in June 2011 and delivered his judgment in August 2013.
He issued it two weeks after responding to a complaint lodged with the Judicial Conduct Commissioner.
Judge Colgan blamed the delay on the Christchurch earthquake, both in his explanation to the commissioner and in the substantive judgment issued last year.
"I regret the delay," the judgment said. "That has come about because of additional pressures on the court's already stretched judicial resources following the Christchurch earthquakes. I apologise to the parties for that delay."
A Ministry of Justice spokesman said he could not elaborate on the reference to the Christchurch earthquakes because the judgment had to stand for itself.
The case involved Ideas Services, an organisation providing support for people with intellectual disabilities.
It dismissed its Southland manager, William Clark, in April 2009. The Employment Relations Authority upheld the dismissal. Mr Clark challenged that decision in the Employment Court and the hearing was held from June 27 to June 29. When the judgment was issued in August last year, Judge Colgan found the dismissal was unjustified and awarded Mr Clark $15,500 compensation.
Ideas Services turned to the Court of Appeal on several points, one of them being that the delay of 26 months affected key findings.
While the Court of Appeal was critical of the delay, it did not give Ideas Services leave to appeal in a decision last week.