The accusations have come from activist Wayne Colquhoun, who claimed in a letter to the DCMS that English Heritage chairman Neil Cossons was compromised due to his affiliation to National Museums Liverpool, which is the client on the project.
Cossons is a trustee at the museum body, and despite Colquhoun's finger-pointing, has been given full backing by the government office.
In response, a DCMS spokesman said: 'As a trustee of National Museums Liverpool and as chairman of English Heritage, Sir Neil is required to make a declaration of his interests to both bodies, and these are on public record.
'In addition, prior to every meeting, all members are required to declare any conflicting interests within the items set out. Where the proposed Museum of Liverpool has been discussed Sir Neil has withdrawn from discussion on every occasion.
'I am very clear that Sir Neil has adhered to correct practice in keeping his two roles distinct and avoiding any conflicts of interest.'
Colquhoun has been at the centre of many disruptions during the long and drawn out dialogue surrounding 3XN's museum design.
Most recently, he was successful in securing a visit from UNESCO World Heritage officials, despite construction work being scheduled to start on the scheme in the coming months.