But he insisted the Scottish Government was seeking to address any shortfall amid concerns youngsters from disadvantaged areas were losing out because they did not have access to digital devices or broadband.
Holyrood's education committee was told on Wednesday there were "deep concerns" among parents about the engagement their children were having with education while at home.
It comes after a report from Poverty Alliance this week warned of a growing "digital divide" in Scotland between affluent families who have access to laptops and computers for their children and those from more deprived areas who do not.
Mr Swinney told the committee there had been "variability" in the effectiveness of schools delivering education even before the pandemic.
"I would have to accept at the outset that there will be inevitably variation in the pandemic environment through remote learning where there will be variation in the education system,” he said.
"It is a very wide and diverse system."
The Education Inspectorate is publishing weekly reviews on remote learning, setting out some of the problems, which is all assessed by the Education Recovery Group.
But Mr Swinney said: "I think it's been pretty much acknowledged widely across the education system that what is being delivered in terms of remote learning now is a significant enhancement on the performance that was delivered in the spring of last year when we dealt with an emergency situation.”
He went on: "It's not perfect, I'm candid enough to accept that, but it's much better than it was last spring."
The education secretary said he was not seeking to implement a system where pupils learning at home would be "sitting in front of a computer all day”.
A data exercise undertaken by ministers last year identified 77,000 Scots youngsters who did not have sufficient digital access, Mr Swinney said.
About 25,000 Chromebooks and iPads were allocated to councils to distribute, although councils were also allowed to use their separate funding streams to procure their own devices.
Mr Swinney said: "The data I have available to me indicates that 77,000 needs have been met through a combination of devices and connectivity packages.
"We're obviously working with local authorities and local authorities are working with schools to enable any further issues to be addressed."
Tory education spokesman Jamie Greene raised concerns that many pupils were losing out while schools are closed.
"We're finding that anecdotally the levels of participation and the quality of remote learning does very from council and even from school to school within local councils, “ he said.
"I do appreciate that these are matters for local councils in terms of distribution of digital devices and so on, but the reality on the ground is that many parents are contacting members of the committee and I'm sure all MSPs with deep concerns about the engagement they are having with education whilst their children are at home."