The latest concerns on performance in some subjects come as an OECD report reveals how pupils in Irish primary schools have spent far less time being taught maths and science than the international average.
The information was gathered in 2008 and 2009, when Irish nine to 11-year-olds spent 12pc of their time on maths, compared with an OECD average of 16pc.
Irish nine to 11-year-olds also spent only 4pc of their tuition time on science, less than half the OECD average of 9pc.
In contrast, they spent 10pc of school time on religion, more than double the OECD average of 4pc.
The figures are included in the latest OECD Education at a Glance report, which provides comparable national statistics measuring the state of education worldwide.
Changes being introduced as part of Mr Quinn's plan aim to improve numeracy and literacy and are expected to push the Irish figure above the OECD average this year.
Mr Quinn pointed out that one of the positive aspects of this year's Junior Cert results was an upward trend in the numbers taking higher-level papers in both subjects.
"The good news is that more candidates feel confident enough to attempt the higher-level papers in maths and science," he said.
He said an increase of 70 minutes per week for maths in primary schools would bring the proportion of time spent on the subject from 12.8pc to 18pc.
He also said it was not just the quantity of time spent on particular subjects that was important, but also what is being taught and how it's being taught.
The Irish National Teachers' Organisation (INTO) said more time for maths teaching had to be accompanied by proper teaching resources, teacher professional development, better textbooks and digital content.
On science, Mr Quinn said Irish students performed above the OECD average.
However, Tony Donohoe, head of education policy with the employers' organisation IBEC, said that the drop in performance in Junior Cert science would cause concern to businesses.
Only 41pc of students taking the honours paper achieved an A or B grade compared with 45pc in 2010.
"This is not surprising in the light of OECD data which shows that Irish nine to 11-year-olds spend only 4pc of tuition time learning science compared to an OECD average of 9pc," he said.