A subsequent investigation also found apparently high numbers of personal calls were being made on his landline and cellphone.
Shanmuganathan had previously been warned about his email and phone use, including in February 2007, when he received a final warning over misuse of the company's 0800 faults number. That warning was valid for two years.
He also had to repay the company $7500, had his pay cut by $10,000 and had to apologise to control room staff over the issue.
His manager, Gary Pritchard, had also emailed Shanmuganathan about his email traffic on October 6, 2009, October 13, 2009 and July 29, 2010.
Appleton ordered Powernet to reinstate Shanmuganathan, effective yesterday, as he believes he has a "tolerably arguable case that he will prove his case of a personal grievance of unjustified dismissal".
His reasons for the finding included doubts over the thoroughness and accuracy of Powernet's analysis of Shanmuganathan's email; its own report showed at least 20 staff had greater web usage than Shanmuganathan, and four other staff had sent more emails than him during the time sampled.
"A number of olders were shown to me which I understood to be print outs of the sample emails to and from the contact organisations, together with some attachments and spreadsheets found on [Shanmuganathan's] computer," Appleton said.
"However, many of the emails were historical, some dating back to 2004, whilst several were dated 2010. This did not accord with the stated sample period of January to September 2011."
An employer relying on large volumes of data to show serious misconduct must take reasonable steps to ensure that data was transparent and fair, he said.
"The documents put before me raised a number of questions as to the fairness of the process followed by the respondent when it reached the conclusion that there had been such a volume of personal email activity that it overreached the boundary between what may be misconduct and serious misconduct."
Shanmuganathan's indication he would accept reinstatement on certain conditions, and his suggestion before being dismissed that he be given a final warning both showed he accepted he had "overstepped the mark in his computer and telephone usage", Appleton said.
Shanmuganathan and PowerNet chief executive Martin Walton both declined to comment ahead of the full hearing.