Ireland's police watchdog has launched a criminal investigation into allegations that the Garda Siochána is secretly reading journalists' phone records, as the Irish government reels from revelations that the police force also regularly records calls to its own stations.

Amid calls on Wednesday for the justice minister, Alan Shatter, to resign, the ruling coalition in the republic also announced an inquiry into the covert recording of phone calls at Garda stations.

The political row over the secret recordings and the treatment of two Garda whistleblowers who were alleging corruption has already claimed one major casualty this week: the resignation on Tuesday of Ireland's top police officer, the Garda commissioner, Martin Callinan.

With the Taoiseach, Enda Kenny, fighting off accusations in parliament on Wednesday that he effectively sacked Callinan, the Fine Gael-Labour government faces calls to extend the inquiry to cover journalists' claims that Gardai were secretly monitoring reporters' phone calls.

The author and investigative reporter Nicola Tallant produced a letter from the police watchdog – the Garda ombudsman's office – confirming it was investigating her allegations that copies of her 02 mobile phone records have been seized over a four-year period.

The letter from the Garda ombudsman says his office regards her complaint as admissible and has decided it will be dealt with as a criminal investigation.

Tallant told the Guardian she was "100% certain" the Garda have been reading phone records.

Since the imposition of the 2005 Garda Siochána Act, the force has been accused of scanning calls of reporters to establish if they have been talking to individual officers.

"I am 100% certain that my O2 records have been seized and read by Gardai. And I am prepared to speak publicly to any inquiry the government has established and be questioned about this," Tallant said on Wednesday.

"This all began in April 2010, I understand, after I started investigating corrupt practices in the Garda witness protection programme for the Sunday World newspaper. I do not believe regular rank and file Gardai are involved in this but rather an elite group of people at the top who just do this kind of thing because they can."

Since the 2005 legislation, senior figures in the force have operated a "Hooveresque" (after FBI boss J Edgar Hoover) monitoring of crime journalists' contacts, she said.

"The only excuse the Garda, the senior elite who are behind this, can have is that they were looking at my phone records as part of a serious criminal investigation. But after four years there is no evidence out there of any serious criminal investigation in relation to my calls and records.

"If the government is serious about cleaning this affair up they should extend their newly announced inquiry to include my allegations and those of other investigative or crime reporters that might come forward.

"This is our equivalent to the phone-hacking scandal that led to the Leveson report in the UK. Only in our case it's the state itself and not a newspaper which is hacking into the phone records of reporters."

During angry exchanges in the Dail on Wednesday between Kenny and the main opposition leader, Micheal Martin, over Callinan's resignation. Martin accused the Irish premier of effectively sacking the state's top police officer.

"You essentially sacked him," Martin said. "You sent a senior civil servant out to the commissioner the day before the cabinet meeting."

Kenny countered by stating: "I reject your assertions. It's actually beneath you to come in here and say something like that."

Callinan announced he was standing down as head of the Garda Síochána after a controversy over driver penalty points.

Two whistleblowers have made repeated allegations that fellow Garda officers routinely wiped penalty points for road traffic breaches for well-connected people. The commissioner had described these claims to a parliamentary committee as "disgusting".