The HSE has said around 7,000 invoices from its suppliers are now overdue or due for payment by tomorrow, as a result of delays it is experiencing in processing payments while it implements a new system.
The executive said it knows the current delays are causing real problems for some suppliers and has apologised to them for inconvenience or difficulties being caused.
But one supplier, which did not wish to be named, has told RTÉ News that the payment delays are now threatening jobs in the business.
The firm is owed tens of thousands of euro across more than two dozen invoices dating back to the end of March and significant attempts it has made to contact the HSE chasing payment have been met with no success.
The issues have arisen as a result of the roll-out of the new centralised €82 million Integrated Financial Management System (IFMS) for the health service.
It will replace multiple, fragmented legacy systems and will be rolled out to all health and social care services provided directly by the HSE, as well as voluntary organisations exclusively or almost exclusively funded by it and others that receive funding from it, along with Tusla.
The system went live in the HSE East area and across its corporate services on 3 July as part of the first implementation group phase.
This includes Connolly Hospital in Blanchardstown, Naas General Hospital, St Columcille's Hospital in south Dublin.
Tusla is also included in the initial roll-out phase, along with other HSE corporate services units.
The next phase, which includes HSE West, will not begin until January, with the roll-out continuing across other regions and services until 2025.
The HSE has described the delays in processing the invoices as "temporary".
"A significant proportion of the current temporary delays relate to transactions which began under a number of old systems and are now being processed by the new system," it said in a statement.
"These invoices need manual validation to allow them to be processed by the new system and this takes time and has led unfortunately to the delays."
"There is no issue or "glitch" with the technology. Once we get to a point where we are only processing invoices issued under the new system, this problem will end."
The HSE added that it is working to minimise delays and is prioritising invoices from suppliers who may be facing particular pressures.
Around 2.1 million supplier invoices are processed by the executive each year for payment.
Small business representative organisation, ISME, said small firms rely on the State to be a banker when it comes to prompt payments.
"It is very serious for SMEs if one of the largest purchasers in the State is extending payment terms," said ISME Chief Executive Neil McDonnell.
"There's a huge onus on the State to ensure cash flow for small business is maintained."
Since 2009, the Government has had a non-statutory requirement that suppliers of departments should be paid within 15 days.
Under the Prompt Payment of Accounts Act 1997, suppliers of services to Government must be paid within 30 days of receipt of an invoice.
