A ban on travel in and out of level three and four areas “doesn’t sit easily with anybody”, the First Minister said.
The restrictions on movement will be entered into law from Friday in a tightening of the rules.
While police will not be putting up roadblocks or stopping vehicles they suspect to be violating regulations, some have railed against the plans – with a Lib Dem MSP describing them as “draconian”.
Speaking at the daily briefing, Nicola Sturgeon said she understands people’s concerns over the restrictions.
She said: “Let me be very candid – I know that it doesn’t sit easily with anybody, including me, to be told that you can’t travel freely within the country, I absolutely understand that.
“But many countries have restrictions like this in place right now to help stop the virus spreading from area to area and that’s particularly important in Scotland where we are deliberately trying to take a more localised approach, we are trying to avoid the whole country having to go into level four restrictions.
“To be blunt, we can only keep relatively low levels of restrictions in areas with low levels of the virus if we ensure that people don’t travel to these areas from other parts of Scotland with high levels of the virus.”
Earlier, deputy first minister John Swinney stressed people travelling between council areas for essential journeys – such as a hospital appointment – will not have to show paperwork if they are stopped.
He said: “If an individual happened to be stopped by the police, which I think is a very, very unlikely circumstance, on their way to a hospital, if they were to explain to a police officer they were going to hospital for a critical appointment that would be an end of the matter.
“They don’t have to have paperwork to substantiate that.”
He added he does “not envisage those circumstances happening”.