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PHB is a non-profit organisation which connects orchards and vineyards with RSE workers.
Evans' apology follows the publication of an article about the mistreatment of a trio of Solomon Islands fruit pickers.
The mistreatment was revealed in an audio recording involving the group and a man, allegedly the general manager Anthony Rarere, threatening to withhold allowances, report the trio to Immigration NZ and withhold assistance to get flights home.
On June 19, the trio met with Rarere, along with six other RSE workers and the meeting was recorded by one of them.
"You've got no ****ing respect. You're only here because of me," he says in the recording.
"If you want to go and stay somewhere else pack your bags and **** off.
"I'm going to call immigration and tell them you've absconded. Look that up, find out what that means.
"The next step, they call the police, they find you, and then they can hold you in the cells until you go home, in August.
"The more you muck me around, the longer I'm going to wait to put you on the list to go home."
The workers subsequently made a complaint to the Ministry of Business Innovation and Employment's Labour Inspectorate.
However, the handling of the complaint was scrutinised after MBIE initially used an investigator with a conflict of interest.
Another investigator was appointed.
The trio hope to return to the Solomon Islands on direct flights this week, but are yet to have any dates confirmed.
Evans said all PHB staff was under "extreme pressure", working long hours to keep RSE staff in employment, accommodation, as well as providing food allowances when they're out of work.
"We have also been finding ways to repatriate our RSE workers to their home countries," he said.
"The pastoral care of our RSE staff is a very important part of PHB, so we are very disappointed that this situation has arisen.
"Although it isn't an excuse, Covid-19 has created an extremely difficult situation for everyone in New Zealand, both for Kiwis but also for those living and working here, away from their families."
Evans said he understood the frustration felt by the RSE staff because a number of them were unable to return to their home country.
"The implications of the pandemic has created a great deal of frustration and confusion," he said.
"We will be updating our RSE staff on the process of repatriation and we will be reassuring all of them that we will be making this happen as quickly as possible.
"We have also immediately stepped up our efforts to check on the wellbeing of all our RSE staff to ensure that all their immediate needs are being met, including food and accommodation.
"Lastly we will be conducting a thorough investigation into all our internal processes."
PHB's top priority was ensuring the welfare of all of employees during these unprecedented times, Evans said.
"Our RSE staff are valuable and highly regarded members of our Pick HB family and their wellbeing is our utmost priority," he said.
Pick HB continues to provide and offer accommodation to all its RSE staff.
"Due to RSE regulations any staff including those that are dismissed can not take up any other offer of accommodation," Evans said.
"If they are moving to other accommodation it has to be approved accommodation by the MBIE labour inspectorate."