Residents in Luton and Blackburn have been told lockdown measures set to be eased this weekend will not be lifted in the towns.
Public Health England (PHE) data released on Thursday showed both had been marked as "areas for intervention" due to a spike in cases.
Leaders of both town councils said they would postpone the planned lifting of certain restrictions.
Gyms and leisure centres in the rest of England are due to re-open on Saturday.
The leader of Blackburn with Darwen Council said it had already decided to keep leisure facilities closed.
Health officials in the Lancashire town had said a phased lockdown could happen if the virus rise was not halted by Monday.
Council leader Mohammed Khan said: "We feel that accelerating our control measures in this way will assist us to move out of having higher Covid-19 rates even faster- we are grateful for the government's help in our local plans on this"
Mr Khan added that the decision to delay the reopening of council leisure facilities would run alongside new "localised prevention measures".
"We feel that accelerating our control measures in this way will assist us to move out of having higher Covid rates even faster - we are grateful for the government's help in our local plans on this," he said.
The steps being taken in Blackburn and Luton should come as no surprise - there has been growing concern about the rising number of cases in each area.
But these are still relatively low levels of infection - Leicester had twice the rate of Blackburn at the point a local lockdown was announced there.
And we should expect to see more of this sort of thing in the coming months.
The widespread availability of testing means in the fight against the virus authorities should be able to spot local flare-ups early and take action to prevent them spiralling out of control. Similar measures are being taken in other parts of Europe.
It is short-term pain for long-term gain.
Luton council leader Hazel Simmons said: "The safety of the public is the priority for us. Not opening the the gyms is part of our ongoing work to tackle coronavirus.
"Better not to open or delay opening than open and then having to close.
"Fighting coronavirus is everyone's responsibility. Too many families and friends have lost loved ones and we must do everything we can to ensure more lives aren't wasted unnecessarily.
"There has been too much heartache in the town for us to risk further anguish, pain and suffering."
Earlier, Luton Borough Council sent residents in certain postcode areas an "urgent message" urging them to get tested for coronavirus due to a rise in cases in the town.
The National Covid-19 Surveillance Report said an area of intervention was one "where there is divergence from the measures in place in the rest of England".
It said these areas have a "detailed action plan in place" because of "the significance of the spread" of coronavirus.
The report said Leicester and nearby Oadby and Wigston continued to be areas of intervention.
Meanwhile Pendle, near Blackburn, has been described as an area of enhanced support, while Calderdale, Northampton and Rotherham have become "areas of concern".
NHS Test and Trace chief Baroness Dido Harding told the BBC there were still concerns surrounding northern towns including Blackburn, Bradford and Leicester.
She said Bradford had been in the "enhanced support" category - one level below an area of intervention.
A drop in cases saw its alert level lowered to an "area of concern", she added.