Mr Williamson, then education secretary, was reported to be the instigator of a party held at the department's Whitehall offices while London was under Tier 2 measures on December 10 last year.
However a Government source told the Express & Star that Mr Williamson did not host the party.
The party was held despite restrictions banning any social mixing between households, with a spokesman for the department admitting a work-related "gathering" had occurred in breach of social distancing rules.
South Staffordshire MP Mr Williamson is said to have organised the event to thank staff for their efforts during the pandemic, however the Government source denied that he had hosted a "party".
Meanwhile Boris Johnson has apologised and a senior aide has quit over footage showing Number 10 advisers joking about a Downing Street Christmas party during the coronavirus lockdown.
Both events are now set to form part of an inquiry, according to a top civil servant.
Susan Acland-Hood, permanent secretary at the DfE, admitted that she attended the DfE gathering where there were drinks and food in the department’s canteen.
She told MPs that if any DfE staff, including herself, were found to have broken the rules then they would face disciplinary action.
When asked about the reports during a Public Accounts Committee (PAC) hearing, Ms Acland-Hood said the gathering for staff was attended by around “two dozen” people – including herself and Mr Williamson.
She added that the event would form part of the Cabinet Secretary’s investigation into a gathering in Number 10 during the same month.
Ms Acland-Hood said: “While this was a work-related gathering, looking back we accept that it would have been better not to have gathered in this way at that particular time.”
She told MPs that the gathering at the DfE office was instigated by Mr Williamson as he wanted to “thank staff” for their work during the pandemic.
Her comments came as Boris Johnson ordered an investigation into claims Downing Street staff broke lockdown rules by holding a Christmas party on December 18 last year – when London was in Tier 3.
At Prime Minister’s Questions on Wednesday, Mr Johnson said he had asked Cabinet Secretary Simon Case “to establish all the facts and to report back as soon as possible” and he said if rules were broken then there would be “disciplinary action for all those involved”.
Ms Acland-Hood told MPs: “I have spoken to the Cabinet Secretary and the gathering that was held will be part of his consideration as part of the investigation that was announced in PMQs.”
Addressing the committee, she said “drinks and snacks” were brought to the gathering at the office by attendees, but “no outside guests” were present.
When asked if it was an organised event, Ms Acland-Hood added: “It was to some extent in the sense that the Secretary of State had said he wanted to thank staff together for the work that they had done.”
A spokesman for the Department for Education said: "On December 10, 2020, a gathering of colleagues who were already present at the office - and who had worked together throughout the pandemic, as they couldn't work from home – took place in the DfE office building in London at a time when the city was subject to Tier 2 restrictions.
"The gathering was used to thank those staff for their efforts during the pandemic. Drinks and snacks were brought by those attending and no outside guests or supporting staff were invited or present.
"While this was work-related, looking back we accept it would have been better not to have gathered in this way at that particular time."