A South Waikato dairy farming company has been fined more than $30,000 for discharging effluent - its second punishment in four years.

Fernaig Farms (2006) Ltd was handed down a fine of $33,750 after being prosecuted by the Waikato Regional Council in the Rotorua District Court.

However, the company didn't appear too happy about the council investigating as staff were "obstructive" to those trying to carry out inquiries at the Lichfield property.

"This has been very disappointing behaviour," said the council's investigations manager Patrick Lynch.

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"It is relatively rare for someone to be prosecuted for a second time for doing environmental harm. Generally, people learn from the first experience and ensure it does not happen again.

"It is particularly disappointing to have a leading farming entity that owns a number of farms and should be setting an example of how to do things right," Lynch said.

"Another concerning aspect with this case was the obstructive behaviour aimed at the council staff who were tasked with inspecting the farm property. They were responding to a complaint that effluent was being poorly managed and were only doing their job.

"Certainly the people on the farm on this occasion made it a difficult and unpleasant experience, sufficiently that police were called to enable the inspection to be carried out."

Fernaig own many farms in the area including four dairy farms.

A prosecution in 2013 also resulted in convictions and a fine of $30,000 for effluent mismanagement on their Mangakino property.