The regional health authority has established an independent inquiry to review the implications of the guilty verdict and said it would not reinstate Allain until the investigation was complete.
Allain, who is suspended on full pay, will remain as professor of transfusion medicine at the University of Cambridge.
He issued a statement yesterday saying: 'I understand that the judgment in Paris may raise concern to the British public about my ability to carry out my duty as the director of the transfusion centre.
'I have therefore decided to step down from my clinical responsibilities until an appropriate committee of impartial and qualified professionals examines the evidence and provides an independent opinion to guide the regional health service.
'I am absolutely confident that through this process my professional integrity and personal honour will be fully restored.'
Sir Colin Walker, chairman of the regional health authority, said the verdict comes as a 'severe disappointment' to Allain's colleagues. 'The issues involved are complex and the Regional Health Authority is bound to look carefully at the written judgment. We share the concern of everyone for all those so tragically affected by HIV.'
Alasdair Liddell, general manager of the health authority, said he hoped the inquiry into the Paris court case would resolve the matter as quickly as possible.
The university's vice-chancellor, Sir David Williams, said: 'Professor Allain is an academic of distinction who is held in high esteem by his peers in this country and abroad.
'We will, of course, be looking at the judgment in the case. We are also taking into account the likelihood of an appeal in Paris.'
Robin Carrell, professor of haematology at Cambridge, said the verdict has been greeted with 'dismay and total shock'. He added that Allain had received support from leading figures in blood transfusion. He believed the inquiry would vindicate the professor. 'In the end people who are right and have fortitude triumph, and that will take place.'
Professor Carrell added: 'There is resolve among all his colleagues from the university and the region to support him in this work no matter what the level of harassment from France or in the future from this country.'
Commenting on the running of the French tribunal, Professor Carrell said: 'Reports I have received from Paris do not give me confidence in the ability of the tribunal to reach a fair decision on this very complex matter.'
Professor Carrell said that Allain had received a unanimous motion of confidence from all haematologists in the East Anglian region.
'The trial in Paris was on a diffuse charge. He answered it point by point. There was on the French tribunal no person from an expert background.'
Allain said he had been made a scapegoat. 'It's very clear I was rounded up. They needed some people (to accuse).'Reuse content