The Inland Revenue is having to keep paper-based employee records and limit access to an online HR system because it cannot cope with demand.
The e-HR system was introduced to allow employees to view payslips and update personal data online, and let managers record and book sickness absence and holidays.
However, an internal Revenue memo seen by Personnel Today sister publication Computer Weekly said: "We recognise that some people may need to keep a temporary paper record of their absences, but these must be entered on e-HR as soon as possible.
"Until further notice, only managers should use e-HR on a Monday. This does not mean that managers should use the system only on a Monday, but freeing space on the system that day should give managers a better chance of completing actions to clear the backlog of approval requests [for holiday and absentee records] and set up substitutes if they have not already done so."
Despite the restrictions on the use of the system, the Revenue denied there was an ongoing problem with e-HR.
A Revenue spokesman said, "Our e-HR system is working as normal. The system has been considerably upgraded recently, which has created much more demand on certain days. There have been occasions when the system has not been as fast as we would like, though this is down to increased use at particular times.
"The e-HR system will considerably enhance our human resource functions, reduce the administrative burden on our managers and give staff and management access to information much more quickly."
Graham Steel, senior national officer at public sector union PCS, said problems with the system were hindering HR staff.
"The systems cannot cope with the normal degree of access. It is becoming very difficult for the HR teams to keep records up to date," he said.
Together with uncertainty about the future of the HR function, computer problems were creating low morale in the department, Steel added.
The Inland Revenue employs 68,000 people in more than 400 locations across the UK. The SAP e-HR system operates with a limit of 3,600 people using the system at the same time, the memo said.
The e-HR system has been introduced in phases since July 2003. This spring will see the addition of an induction package for new recruits and a facility for claiming travel expenses.