In April, Nandy said the 68-year-old sports media rights executive was the “outstanding candidate” to fill the position, despite not being on the original three-person shortlist.
She has now removed herself from the final decision, delegating responsibility to the Sports Minister.
Last month, Kogan told MPs on the Culture, Media and Sport Committee (CMS) during a pre-appointment hearing that he was being “utterly transparent” by declaring his donations.
The committee endorsed Kogan, but said he must work to “reassure the football community that he will act impartially and in a politically neutral way”. Committee chair Dame Caroline Dinenage warned that Kogan’s “past donations to the Labour Party will inevitably leave him open to charges of political bias in a job where independence is paramount”.
Kogan said he had donated “very small sums” to the campaigns, as well as thousands of pounds to Labour MPs and candidates in recent years, but had “total personal independence from all of them” and pledged “total political impartiality” if appointed.
A DCMS spokesperson said: “We have received the letter from the Commissioner for Public Appointments and we look forward to co-operating fully with his office.
“The appointment is in the process of being ratified in the usual way.”
Kogan declined to comment.
It has also emerged that Nandy has written to the CMS Committee and told them: “I heard clearly the Committee’s comments regarding David’s transparency and candour regarding previous political donations that he had made and the need for him to take concrete steps to avoid the perception of any bias or lack of independence from government.
“As a first step to avoid any risk of this, I am writing to inform you that I have delegated the final decision on the chair’s appointment to the Minister for Sport.”
Stuart Andrew, the shadow culture minister, said the appointment of Kogan was “Labour cronyism” and added Nandy “belatedly” stepping aside was “a necessary move that highlights just how compromised this selection has become”.
“The public has a right to know whether this was a fair and impartial process, or yet another case of political patronage disguised as due diligence,” he said.
“The decision to launch an inquiry is welcome. [It] must include scrutiny of Keir Starmer, his advisers, and whether any conflicts of interest were properly declared.”
A spokesman for the Prime Minister added Kogan had been appointed through a “fair and open competition”, and the BBC has been told his donations were below the threshold that requires declaring.
The Football Governance Bill, which is currently passing through Parliament after being reintroduced by the Labour government in October, will establish a first independent regulator for the professional men’s game in England.
The legislation will hand power to a body independent from government and football authorities to oversee clubs in England’s top five divisions.
Kogan – a former BBC journalist who also previously advised the Premier League, EFL and other leagues on broadcast rights – said he wants to put “fans at the heart of the regulator” and help the football pyramid.