Oxford is to be placed under tier 2 Covid-19 restrictions after a rise of cases in the city.
Oxfordshire County Council said the central government decision followed "intensive discussions" between the local authorities and MPs.
The number of cases in the city per 100,000 rose to 137.1 for the week ending 23 October.
The new rules come into force from Saturday. The rest of the county will remain in tier 1.
Council leaders have been pushing for a move to tier 2 since last week.
Ian Hudspeth, leader of Oxfordshire County Council, said it was the "appropriate moment" for the tier change but expressed serious concerns the rest of the county had not followed suit.
"We are deeply disappointed that despite clear evidence showing the virus is now spreading to older and more vulnerable communities across the county, our request that Oxfordshire as a whole should move to tier 2 was not approved," he said.
For Oxfordshire as a whole, the most recent rate was at 117.5 per 100,000 people.
The authority said the virus was spreading "to a much wider age range across the county and is no longer confined to younger people in urban areas".
All six Oxfordshire councils supported moving the entire county into tier 2.
Bruno Holthof, chief executive officer at Oxford University Hospitals NHS Foundation Trust, said: "We have moved from a position of low and stable hospital admission rates over the summer to one in which admission rates are increasing.
"We know there is a time lag between rising cases and an increase in hospital admissions, and so we expect to see a further increase in hospitalisation rates over the coming weeks."
Susan Brown, leader of Oxford City Council, said the decision not to put the whole county into tier 2 was "shocking", adding "the spread and case numbers outside the city are also of grave concern... when so many people commute into our city".
Anneliese Dodds, Labour MP for Oxford East, said: "I am sure people in the city will take these new measures very seriously and I urge everyone to comply."
But she said she was "concerned that evidence of the need for steps to be taken across Oxfordshire has not been taken on board" by the Department of Health, which has been contacted for comment.
In a joint statement the county's four Conservative MPs, Robert Courts, John Howell, David Johnston and Victoria Prentis, said: "Public health is the priority and we hope this will stop the spread of the virus.
"We do not want to see the rest of Oxfordshire put into tier 2, as council leaders have been requesting, if it can be avoided and given the impact this would have on individuals, families and businesses.
"We therefore strongly urge everyone today to redouble their efforts... and help prevent the rest of the county needing to be placed into tier 2."