Bedford Hospital chief executive Ken Williams had known for several years about the practice of using the chapel of rest as a temporary mortuary, which caused outrage when photographs of seven bodies wrapped in sheets on the floor were published in the press.
Mr Williams resigned on Monday after the scandal was leaked to the media by Unison regional organiser Willy White.
The situation was brought to Mr White's attention by hospital staff who were worried about the implications of raising the matter internally.
A temporary mortuary had been taken out of service after a porter hurt his hand on the door.
A preliminary internal inquiry has indicated that the situation arose from management failure, and that underfunding was not an issue.
Mr Williams confirmed that he had been aware of the use of the chapel in the past, and a spokesperson for the trust confirmed that he had been aware of this for some years.
Mr White said that he had been told the practice had been used every winter in recent years and that although there was clearly a problem with a lack of mortuary capacity, managers had done nothing to rectify the situation permanently.
He said: 'Why should we have to point out that it is inappropriate to handle bodies like this? One of my sources says it has been going on for about four years.
'If existing mortuary facilities were under pressure, why did they not make an emergency capital bid?
'This is about poor management, very poor decision-making.
The very clear impression I have is that it happens every winter.'
Just hours before the chief executive stepped down, Mr White told HSJ: 'The buck stops on Ken Williams' desk.'
The Commission for Health Improvement is currently undertaking a clinical governance review of the trust and a team is due to visit the hospital as part of this in the next two weeks.
The review will 'take into account' the media coverage of the issue in making its report.
The Health and Safety Executive was due to visit the hospital this week to look at the potential health hazards of storing the bodies in the chapel.