Frances Fitzgerald was speaking in the Dáil during a debate about tighter regulation of the sector
The Tánaiste has said she is 'deeply concerned' by recent revelations about Console and other charities.
The comments were made during a Dáil debate on a motion from the Social Democrats and the Green Party tonight calling for better governance of agencies receiving state funding.
Responding to the motion, Francis Fitzgerald said: "I am deeply concerned by the recent revelations about Console and other charitable organisations. The public must have confidence that the money they donate to charity will be managed and used correctly at all times."
The Justice Minister also told the Dail that the Charities Regulator now has 12,500 different bodies on its register.
She also outlined how it had received around 300 concerns raised against 132 organisations - ranging from people raising questions over the purpose of a given charity to the quality of service provided.
The Tánaiste said she was working with the regulator to ensure it has the staff it needed to investigate allegations of wrongdoing, adding that all necessary extra staff will be in place by September.
Sinn Féin leader Gerry Adams observed: “There is an onus on the State to provide the requisite oversight and accountability to ensure charities operate within parameters that don’t allow for the blatant waste of public monies and the well-meaning donations of citizens."
Deputy Stephen Donnelly says he has concerns some charities are being set up potentially to facilitate tax avoidance.
"What the regulator needs to be doing is saying 'why are private companies, set up to make a profit, being owned by charitable trusts?" he argued.
Meanwhile, it was confirmed that the Department of Health has begun a full external review of all so-called 'Section 38' agencies.
The Dáil has been told that external consultants are now looking at the agencies that are in receipt of taxpayer funding.
Six of the 40 such agencies are already subjected to the review - but the Health Minister says they will all be completed.
Simon Harris says he wants to be sure that every one of them are operating properly.
"I'm not satisfied that we just have an internal HSE review - I want to bring in the external layer," he said.
"I want to have independent, external consultants go in and examine all Section 38s - make sure that they're all not just signing on the dotted line to say they're in compliance, but they're actually in compliance."