Dublin's Tallaght Hospital reported unsatisfactory support from the company, iSoft, "over a number of years", according to a Department of Health document released to the Irish Examiner under the Freedom of Information Act.
The company was responsible for providing software back-up for a patient management system at the hospital.
In 2003, health board chiefs were eager to roll out identical systems nationwide, so that patients' records could be easily computerised and shared between hospitals.
The project was known as the Hospital Information Systems Programme (HISP), and iSoft was declared the preferred supplier in January 2003.
In November 2003, Pat McLoughlin, the then chief executive of the South Eastern Health Board, which was leading the project, wrote to the department urging that contracts be signed with iSoft "without further delay."
But in December that year, the department issued a response to Mr McLoughlin outlining several concerns. In particular, the department sought "evidence that supplier support for the implementation and continued development of the system will be adequate."
"In this context, it should be noted that the AMNCH has reported unsatisfactory support from iSoft over a number of years and continuing into late 2003," the department added.
The acronym refers to the formal name for Tallaght: the Adelaide and Meath Hospital, incorporating the National Children's Hospital.
Because of the hospital's dissatisfaction and other concerns listed in the December 2003 letter, the then Health Minister Micheál Martin refused to sanction the project.
But the health system was subsequently restructured and the HSE established to replace the health boards.
The HSE did not require Department of Health approval to give the project the green light. Instead, in April, it received clearance from the Department of Finance to sign a contract worth €56m over 10 years with iSoft.
The contract covers "software licences, implementation services and software support" for the hospital information system over the period in question.
In a statement, iSoft said: "Whilst it isn't appropriate for iSoft to comment on a letter from the department to one of its health board officials, nor on the detail of any individual contractual relationships with one of our customers, we can confirm that, as a business, we are committed to meeting our contractual obligations to support our customers."
The overall HISP project will cost up to €400m to roll out. The HSE believes the system is crucial to improving patient services.