Children and adults in need of help with speech, eating, drinking and swallowing are on lengthening waiting lists while their therapists have been moved to do swabbing and contact tracing.
Hundreds of public health staff, including speech and language therapists, are being moved by the HSE, leaving under-resourced areas struggling.
The deployment of much-needed specialists was raised by Roscommon Independent TD Denis Naughten as HSE officials appeared before the Oireachtas Health Committee to be quizzed about its testing and tracing system.
Niamh O'Beirne, the HSE's National Lead for Testing and Tracing, said the aim is to have a permanent swabbing and contact tracing workforce so specialists can return to their jobs, but this will take several weeks to achieve.
Around 25 therapists are doing contact tracing and 800 staff from other parts of the public service are involved in taking swab samples. Earlier Ms O'Beirne apologised to the 1,971 people who tested positive from October 16 to 18 and had to inform their own contacts because the HSE teams were swamped.
"Since Friday, October 23, our contact tracing system is back on track and achieving its metric of all close contacts being contacted within 24 hours of the notification of the positive case," she said.
The committee was told that the HSE plans to recruit up to 800 contact tracers, with 60 to 70 new staff to be brought in every week. The committee also heard a small but significant number of parents are refusing to get their children tested for Covid-19 when they are phoned by HSE contact tracers.
Public health specialist Dr Kevin Kelleher said people can be unhappy when told they are a contact of a positive case and they must restrict their movements.
"There is a significant, very small group of parents who refuse to get their child tested and are very unhappy as a consequence of this process," he said.