Ms Sturgeon defended Mr Matheson when Scottish Labour leader Kezia Dugdale highlighted this week’s Inspectorate of Constabulary report, commissioned following the deaths of Lamara Bell,25, and John Yuill, 28.
The couple lay undiscovered for three days by the M9 near Stirling despite a sighting of their wrecked car being reported to a police control room.
The review found examples of call handlers under pressure to end calls quickly and grading of calls dependent on resources available.
Staffing levels at the Bilston Glen call centre were insufficient and resulted in poor call-handling. It identified a lack of staff when work transferred to other locations after closure of police control-rooms in Stirling and Glenrothes, leading to “low levels of performance”.
And staff under “unacceptably high” pressure during critical stages of the changeover.
Ms Dugdale asked Ms Sturgeon if she accepted there had been “systematic failings” in Police Scotland.
She said Mr Matheson had been on the television claiming there had been no systemic failings in the call handling process.
“We now know that simply wasn’t true,” Ms Dugdale said.
Ms Sturgeon again sent her condolences to Ms Bell and Mr Yuill families adding her heart went out to them every day when she thought of the “dreadful circumstances” of their deaths.
The First Minister added that the HMIC report was not specifically into their deaths pointing out that another investigation by the Police Investigations and Review Commissioner (PIRC) into the tragedy had yet to be published.
Ms Dugdale then asked if the First Minister still had confidence in her Justice Secretary.
To applause on the SNP benches, Ms Sturgeon replied: “Yes I do.”
Ms Dugdale retorted saying: “The report by HMICS on Police Scotland’s call handling shows that the transition to a single force has been anything but smooth.
“Despite denials from the SNP Justice Minister, it’s clear that there are systemic failings at the heart of Police Scotland. It’s time for the SNP Government to take responsibility for some of the major police failings on its watch. From the resignation of the Chief Constable to rock bottom morale amongst staff; and from allegations of spying on journalists to a £25 million budget overspend - things have gone badly wrong under this SNP Government.”
Ms Dugdale added: “Nicola Sturgeon said she wants to be judged on her record, but the verdict on policing is damning.”