Boys are to get the HPV vaccine from September.
The Health Minister Simon Harris has confirmed the roll-out of the "vital and life saving measure" will proceed as planned.
He tweeted that resources will be in place and have been provided by Government.
HPV infections can cause cancers of the penis, anus and throat in men.
In a joint statement the IMO, INMO and Fórsa say they are "fully committed" to the rollout of the HPV vaccine to boys.
"There is an issue in respect of adequate staff numbers to provide the extension of the vaccine without increasing the workforce", they say.
"There is currently a recruitment pause, as well as an acute staffing shortage, while in the meantime this rollout represents additional workload.
"The matter was the subject of a conciliation hearing on 18th June at the WRC, following which the HSE requested an opportunity to reflect at conciliation.
"We consider that within this procedure, the HSE must concentrate on bringing forward realistic proposals to ensure the programmes can roll out."
The IMO's Dr Ann Hogan says: "The IMO is concerned that the resources allocated for the HPV for boys will not be sufficient for the successful roll out of this initiative.
"I am concerned at the many unfilled posts and vacancies in Community Health Departments throughout the country."
While Fórsa adds it hopes that the HSE "grasp the opportunity now to put the necessary staffing in place" to properly deliver a much welcome enhancement of public health provision.