Ms Shortall resigned her junior ministry three days ago following months of conflict with Mr Reilly.
Her resignation came after a row over his decision to add a number of locations, including two in his own constituency, to a list of proposed primary healthcare centres.
Speaking on RTÉ Radio, Ms Shortall described the decision by Mr Reilly to include the two centres as stroke politics.
She also said that she felt let down by her colleagues in the Labour Party and that party leader Eamon Gilmore had backed Mr Reilly and not her.
Ms Shortall also said that Minister Reilly blocked many of the reforms that she had tried to implement.
Ms Shortall said she believes Mr Reilly does not subscribe to the Programme for Government and there were fundamental differences between them on how the health service should develop.
Taoiseach Enda Kenny and Mr Gilmore were present at a meeting between Ms Shortall and Mr Reilly, but it failed to resolve the issues.
Ms Shortall also said that Cathal Magee was “driven out of his job” as HSE Chief Executive.
Minister for Children Frances Fitzgerald has defended Minister Reilly following Ms Shortall’s criticism.
Speaking on RTÉ Radio, Ms Fitzgerald said she believed that there was nobody more committed to reforming the health service than Mr Reilly.
She said that the Government will deliver on its commitments in the area of primary care.
Ms Fitzgerald said reforms were being pursued but could not be delivered overnight.
Fianna Fáil’s Billy Kelleher said Ms Shortall’s comments provided “an insight into the malaise” in the Department of Health.