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Despite this, Twyford insists that there was no conflict of interest and the issue was handled "exactly the way his employers expected him to".
Twyford told Newstalk ZB's Heather du Plessis-Allan he was aware that Ebert owned the firm while he was working for his office.
Three Point Two "wasn't actively trading" while Ebert was working fulltime for Twyford.
But Twyford said he was aware that once Ebert was on a part-time contract, "he did some other contract work" through Three Point Two.
The firm advertises "advocacy and lobbying" services helping clients "stay several steps ahead of your competitors and the regulators".
In a statement to the Herald, Ebert said he disclosed this to DIA – his employer – and it was aware of his directorship "from the outset".
He said "no conflict of interest arose" and said that "no Government relations work was undertaken for anyone during the whole period".
In his statement, Ebert said he had undertaken three "short-term research and communications jobs [that] were done for three separate non-government clients between August 2018 and January 2020 to supplement my part-time income".
None of these jobs, he said, were government relations work and no conflict of interest arose.
He would not disclose the names of these clients to "protect their privacy".
A spokesperson from the Department of Internal Affairs confirmed that Ebert was employed by the department as a specialist ministerial adviser to Minister Phil Twyford.
"During Mr Ebert's tenure, a dual arrangement was established with the Parliamentary Service [and Ministerial Services] in order for Mr Ebert to support the Labour Leader's office."
The DIA spokesperson said this sort of dual arrangement was not uncommon.
However, it said that as part of the recruitment process, Ebert informed DIA that Three Point Two had not been actively trading since October 2017.
DIA, the spokesman said, accepted this.
Despite this, the Three Point Two website remains up and lists Ebert as its managing director.
"…Ebert provides almost 30 years public affairs and communications experience in the private and public sectors in New Zealand, Australia and the United States," the website says.
It also lists Ebert's email and mobile phone number on the "contact us" section of the website.
When contacted by the Herald this morning on the phone number listed on the Three Point Two website, Ebert answered.
Companies Office records show that the company filed its annual returns on August 1 last year.
The records show the company is still registered and Ebert is the sole shareholder.
Requests for comment were sought from Twyford, but a spokesperson deferred any questions to DIA.
Ebert worked fulltime between October 2017 and August 2018 and then part-time from August 2018 until January this year.
He left the job in recent weeks.
This is not the first time issues of conflicts of interest at a senior level of Government have been raised.
Gordon Jon (GJ) Thompson, who founded the lobbying firm Thompson Lewis in 2016, was appointed as Prime Minister Jacinda Ardern's interim Chief of Staff in late 2017.
Thompson took a leave of absence from his firm while he was working in Ardern's office, but according to documents released to the Spinoff under the Official Information Act (OIA), Thompson did not identify the names of his firm's clients.
In a statement, Thompson said any potential conflicts of interests were declared and managed at the time.
"I took a leave of absence from the firm. The arrangements made reflected the short-term nature of the role."
Ardern said she was comfortable with how the conflict of interests was managed but National leader Simon Bridges said the situation "did seem wrong".
