His resignation came after an investigation by employment law expert Maria Dew QC, who has led a number of high-profile workplace reviews in the public and private sector.
It is understood that Dew was brought in by the AgResearch board after concerns were raised about Richardson's treatment of staff.
He was accused of bullying behaviour, and several current and former staff members were interviewed as part of the investigation, sources told the Herald.
Dew's investigation is believed to have ended but the findings and even the existence of a report are shrouded in secrecy. It is not known whether Richardson was cleared or whether his resignation came during the investigation or after it was completed.
On October 8, AgResearch published a statement on its website saying that Richardson was resigning and would leave the role by the end of the month.
Chairman Paul Reynolds said the organisation could not comment on matters related to past or present employment agreements because the details were "personal and private".
"As already stated on the public record, Tom Richardson came to a mutual agreement with the AgResearch board to step down from the role of chief executive in October after a three-month notice period."
Richardson declined to comment when the Herald spoke to him.
"As a former employee, I'm still bound by my confidentiality obligations to AgResearch, which stops me from saying anything about confidential or private information about AgResearch."
He said in a statement last month that he had "nine rewarding years" at AgResearch, which focuses on agricultural and biotechnology research and employs around 800 people.
Originally from the United States, he has lived in New Zealand for more than 25 years. Before joining Agresearch, he spent 17 years at the forestry-focused research institute Scion.
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Research, Science and Innovation Minister Megan Woods also declined to comment, saying it was a matter for the board.
Dew is considered a go-to expert for sensitive employment investigations, especially those involving high-profile figures. She reviewed allegations against Retirement Commissioner Diane Maxwell, clearing her of wrongdoing in May. And she is leading one of two reviews into allegations of sexual assault by a Labour Party staff member.
Information released under the Official Information Act shows that the AgResearch board received one formal, written complaint in the last three years. All information relating to the complaint - including who or what it was about - was not released on privacy grounds.
It is understood that some concerns about Richardson were raised through more informal, internal channels and would therefore not show up as formal complaints.
The documents also showed eight AgResearch executive team members have left the organisation since 2016.
AgResearch Finance and Business Performance Director Tony Hickmott - who is now acting CEO - noted that these departures came at a time of upheaval.
AgResearch has been going through a restructuring process which involved nearly 50 redundancies and the transfer of 200 staff from the Hamilton and Dunedin sites to the Lincoln and Palmerston North sites.
Earlier this year, the Public Service Association (PSA) worked with AgResearch to resolve separate allegations of bullying against staff at the Lincoln campus, near Christchurch, which did not relate to Richardson.
"We were troubled by the distressing stories our members at AgResearch shared with us, and deeply impressed by the courage it took for them to stand up and push for change," said National Secretary Glenn Barclay.
Barclay said the PSA had worked with AgResearch staff, leadership and independent investigators to help the institute improve its workplace culture. He said he believed positive changes had begun under a new leadership team at AgResearch.
Reynolds, the chairman, said AgResearch did not have a workplace bullying problem.
"AgResearch refutes any suggestion that our workplace culture does not provide an environment to foster innovation and leading research upon which our reputation is based," he said.
"We have a strong culture of success that is supported by modern internal policies and support mechanisms that help our people thrive and enjoy working for AgResearch."
Agresearch
• Created in 1992, now one of seven Crown Research Institutes (along with Plant and Food, Environmental Science and Research, Scion, GNS Science, Landcare, and Niwa)
• Focuses on agricultural and biotechnology research
• Around 800 staff, mostly based at four research campuses (Hamilton, Palmerston North, Lincoln (Christchurch), Dunedin)
