Taoiseach Enda Kenny said the recording of telephone calls in and out of Garda stations since the 1980s could have an impact on court cases past and present.
Asked if he would tell Mr Shatter to resign over the crisis, he replied: “No.”
He added: “The Minister for Justice on behalf of the Government will continue to reform the justice system, will work now to introduce an independent statutory authority for An Garda Síochána that will bring our system into the modern era.”
Mr Shatter is expected to come before the Dáil on Thursday to answer questions about the controversies.
Fianna Fáil leader Micheal Martin demanded the justice minister apologise for claiming Garda whistleblowers did not co-operate with internal inquiries, while Sinn Féin leader Gerry Adams said the minister had protected the Garda Commissioner “at every turn”.