Reopening schools for all pupils in June was the governments "second-best option" according to Wales' Chief Medical Officer, Dr Frank Atherton.
Speaking at Thursday's press conference, he said the health, safety and well-being of children is the Welsh Government's "top priority" and a number of options had been considered for reopening schools.
He admitted his preferred option was to reopen schools in August to have more time to understand the virus but was faced with opposition from the teaching unions.
Dr Atherton said: "When I was discussing this with the Education Minister, my preferred option would have been to reopen the schools perhaps in the end of summer in August to give us a little bit more time but I understand that was not attractive to the unions.
"So we've got a second-best option which is we're going to reopen the schools towards the end of June for a short period of time with very different arrangements so that can be done safely."
When explaining the reason for easing the lockdown and reopening schools he said the improvement in surveillance system meant they could monitor the number of cases in a more accurate way. He added the number of cases had also dropped from thousands to hundreds which was positive news.
All age groups will return to school on 29 June
The term will be extended until 27 July
There will be a phased approach, with year groups being split into groups with staggered starts, lessons and breaks
There will be no more than a third of pupils present at any one time
Smaller classes which will consist of online and classroom based teaching.
Education Minister Kirsty Williams has tweeted following the press conference to say the decision enables children to have some time in school ahead of the summer break and is fully in line with the latest scientific advice.
She added: "We also explored reopening schools later in the summer but this would have involved a complete structural change to the school year."