Siptu says between 1,500 and 2,000 health workers who signed up to be "On Call for Ireland" were handed agency contracts with inferior terms and conditions.
The trade union says it has been contacted by a number of workers hired under the scheme.
It says the contracts do not include death-in-service benefits which could amount to up to two years' salary for a worker with a direct state contract, or Covid-19 leave pay.
Siptu divisional health organizer Paul Bell says agency staff are taking all the same risks and should get the same treatment.
"These workers because they are not in that pension scheme have no access to any type of cover should they become a fatality and please god that doesn't happen," said Mr Bell.
"We don't want to see a situation where a health worker on that type of contract succumbs to an illness of Covid-19 and then their family and loved ones then have to pursue the State or the employer for some type of compensation."
Mr Bell said that these workers will not be covered for self-isolation should they have to do so.