Speaking on the BBC’s Good Morning Scotland, John Swinney said that the youngest pupils are “very unlikely” to be transmitting Covid-19 and added it was “unlikely” that all students would return at once.
Such a move could see schools reopen in a similar manner to the staggered return of students to university campuses, with those requiring the most face-to-face teaching or at the lowest risk of transmitting Covid-19 returning to school first.
However, the Scottish Government was criticised for ‘drip-feeding’ information around the return of pupils to schools.
Mr Swinney said: "We are looking at all possible avenues to secure the resumption of face-to-face learning and we are looking at the way in which that may be delivered.
"We have said already that that is unlikely to be a binary choice - either everybody in or everybody out.
"It is much more likely to be a phased return where we will look at particular cohorts of pupils."
The deputy first minister added that schools being full added “about 0.2” to the R-number, which dictates how fast the virus is spreading, with that figure reducing when the number of pupils is limited.
Mr Swinney also added that the “challenging situation” for pupils with additional support needs also needed to be met.
On pupils studying towards National 5s, Highers and Advanced Highers he said: "We are also looking at the senior phased pupils because obviously they have certification processes coming up and we want to make sure that they can have access to all the learning and teaching they require to command those certificates."
Scottish Conservative spokesperson on education Jamie Greene criticised the comments after the First Minister “could shed no light whatsoever” on plans during her Covid-19 statement to Holyrood on Tuesday.
Mr Greene said: “After the First Minister said yesterday she could shed no light whatsoever on a phased approach to re-opening schools, the Deputy First Minister has now drip fed vague plans on a radio interview the very next day.
“This endless confusion and lack of clarity is helping nobody. Parents are simply seeking clear messaging from the SNP Government over their plans for schools and what it will mean for them and their children.
“Ten months into the pandemic, asking for a route map towards getting our young people back into classrooms, when it is safe to do so, is surely not too much to ask of the SNP Education Secretary.
“In the meantime, the SNP Government has woefully under planned and under resourced remote learning and left many beleaguered teachers and parents struggling to deliver meaningful but vital education.”
However, the decision to close schools due to the accelerating pandemic made in early January is backed by an overwhelming majority of Scots.
Almost three quarters of Scots aged 16 and over backed the move, but a third said more should be done to support parents with home-schooling.
On Tuesday, Nicola Sturgeon announced schools would stay shut to the majority of pupils until at least mid-February.
The Scottish Government has said schools will open as soon as possible, but that the decision is dependent on community prevalence of Covid-19.