The HSE has ordered hospitals and other groups to stop top-up payments to more than 130 people.
It has told the Public Accounts Committee that allowances to 139 senior officials will be stopped from July 1.
The decision comes after a review of more than 200 business cases sent by the so-called 'Section 38 agencies' who wanted to keep some payments.
The abolition of the allowances will affect senior officials at institutions including Temple Street, St Vincent's, St James's, the Rotunda, the Mater, Crumlin Children's Hospital and the Central Remedial Clinic.
The HSE has written to all Section 38 groups forbidding them from using private income to pay officials above the limits of the public sector pay policy.