Timothy Davies, nine, had received a bone marrow transplant; he died on Wednesday. Belinda Coffey, five, was being prepared for a transplant and died last Saturday.
Their distraught parents last night demanded a full inquiry. Treatment which diminished their immunity left both children vulnerable to a common bacterium, Enterobacter cloacae, which the hospital believes entered their bloodstreams in a feeding solution which should have been sterile.
Two other patients were infected. One was last night 'critically ill' in intensive care; the other has recovered. 'We are confident that no other children in the hospital are at risk and, since the outbreak was identified, no more of this fluid has been made-up at the hospital,' Dr Jennifer Hill, director of public health for Salford and Trafford, said. 'We are confident the source of the infection is definitely not blood, blood products or bone marrow. The feeding solution is not prepared on the wards, and the infection is not contagious.
'We are therefore able to reassure parents and children that the steps we have taken have been successful in controlling the outbreak.'
Two pharmacy technicians are responsible for preparing the feeds. The solutions are meant to be mixed in an area made sterile by air filtration. Ingredients are handled with double-layered gloves in apparatus similar to equipment used for radioactive material.
The bacterium is usually harmless, an organism found commonly in human intestines, and in soil, water and sewage. The technicians and other staff who worked closely with the children were 'very concerned and very upset', David O'Neill, the hospital general manager, said.
Screening of staff had failed to identify the source of the infection. Disciplinary action had not been considered. The feed preparation regime, in use at the hospital for two years, had been checked regularly. 'There were no microbes in the system on Wednesday, and on Thursday there were,' Mr O'Neill said.
Timothy, from Darwen, Lancashire, was re-admitted to the hospital because doctors were anxious that his recovery at home might be jeopardised by infections. Marrow had been donated by his brother, Mark.
Belinda, from Disley, Cheshire, was due to travel to the United States because available marrow donors in Britain were unsuitable.
The hospital also treated Laura Davies, the five-year-old who died in Pittsburgh last year after protracted transplant therapy.
The Royal Manchester, in Pendlebury, was refused trust status last year because of a pounds 2m deficit. Mr O'Neill said that financial remedies had not affected medical standards.
Timothy's father, Peter, said: 'I'd like to shoot the people responsible for this. Something has gone wrong all along the line. We have got to make sure that it never happens again.'
Mr Davies, a factory worker, said he and his wife, Hazel, made the decision to switch off Timothy's life- support machine on Wednesday. 'Tim fought hard to beat leukaemia. He was doing so well.
'When he was at home we had to keep him in isolation and give him vacuum-packed food to prevent infection. He had to go back into hospital to make sure he was free from infection. Can you believe it?'
Ann Alexander, solicitor for Belinda Coffey's parents, said they wanted to mourn their daughter's death in private and would be making no comment.