Shirley Anne Somerville said many people did not register negative tests, but insisted it was an issue she was “keeping a close eye on” ahead of the new academic year.
Data from the week ending June 13 shows there was a 5.2 per cent uptake of tests amongst secondary school pupils, and a 28.1 per cent uptake amongst staff.
Routine testing in Scottish schools began in February, where every high school aged pupil and teachers in all schools were offered free lateral flow tests in a bid to stem the spread of coronavirus in schools.
During the exchange at Holyrood’s education portfolio questions on Wednesday, Ms Somerville blamed the low uptake figures on under-reporting, but admitted she would like to see higher uptake numbers.
She said: “We do believe that there is an under-reporting of Covid testing levels within schools, both from pupils and staff, because there is an under reporting of when a person gets a negative test.
"So certainly, we've discussed this at great length in the education recovery group and that is one of the reasons which both the unions and Public Health Scotland, and other members of the groups think that we are looking at a lower level of results coming through than perhaps is what's happening in the area.
"But it is something which we've been very keen to press and I'd like to thank the unions to for their work to encourage their staff to take that up, and for local authorities to encourage that.
"[We want to] ensure that we're keeping that right up until the summer holidays, and we're already looking at what needs to be done to ensure that testing is high, as we would like it to be as we move into the next academic year.
"But it is something I am keeping an exceptionally close eye on because I would also like to see the figures be higher than they are.”
Mr Marra has now lodged parliamentary questions asking for more details.
He said: “Scottish education has been let down by absent leadership throughout the pandemic. It took too long to get testing established and these figures show little has been done to ensure its effectiveness.
“Greater safety measures such as robust testing could have reduced disruption to young people’s education and increased safety for staff, pupils and families. Thousands of pupils and staff have lost out on classroom time, and some school even forced to close, due to a lack of a robust testing regime.”
Recent figures have shown the number of positive cases of coronavirus in school-aged children are at the highest ever level. Scotland is now recording more than 2,000 coronavirus cases a day, with the vast majority being in younger age groups.