Restrictions on travel to Manchester and Salford will come into force on Sunday, while existing bans on travel to Blackburn, Darwen and Bolton will remain in force.
Rules in place on Bedford and Ireland have now been removed.
Opposition MSPs criticised the new rules as “incoherent and confusing”, as case rates in Manchester and Salford are similar to those in Dundee where there are no restrictions.
Liberal Democrat leader Willie Rennie said: "The Scottish Government have put in place regulations preventing travel to places in England which everyone knows cannot be enforced. Meanwhile travel is still permitted to parts of Scotland where the same levels of cases are being reported… the Scottish Government is tying itself in knots.”
In the week to June 13, there were 333 cases per 100,000 people in Salford, and 328 in Manchester, according to figures from Public Health England.
In the same period that figure was 318 per 100,000 in Dundee, which has the highest Covid rates in Scotland.
South Ayrshire, with the second-highest rate, had 250 cases per 100,000.
Ms Sturgeon said decisions were taken based on risk assessments and the advice of clinicians.
She told a Covid Briefing on Friday: “We take decisions on the basis of risk and relative risk. We've got the levels system in Scotland that determines whether and when travel restrictions are imposed within Scotland.
“I don't want to be imposing travel restrictions anywhere. We're doing this because advised by clinicians we make assessments of how to minimise the risk of more virus coming into Scotland, or people travelling from Scotland exacerbating the situation elsewhere.“As you see today we don't keep them in place for any longer than is necessary.”
Dundee is in level two restrictions, while neighbouring Angus and Perth and Kinross are both in level one.
However, NHS Tayside has extended level two visiting restrictions to hospitals across the region in a bid to reduce virus spread, meaning only one visitor is allowed.
The health board has urged Dundee residents to follow Covid-19 restrictions and take up testing and vaccination, including at drop-in clinics offered across the region.