Wednesday's new outbreak was on a cattle farm near Egham, west of London, 13 miles (21 kilometres) from the farm where last month's outbreak occurred, and 10 miles from the Pirbright government research lab pinpointed last week as the source.
A spokesman for the Department for Environment, Food and Rural Affairs (Defra) said Thursday it was "likely" the virus would be fully confirmed as being the same strain once the tests were concluded.
"We will not be able to confirm the full virus strain until all sequencing is completed. This is currently in progress," he said.
Cattle and pigs on the affected farm were slaughtered and a nearby herd was to be culled, less than a week after officials declared Britain free from foot and mouth and lifted restrictions.
Defra has imposed a new England-wide ban on the movement of cattle, sheep, pigs and other ruminants following the confirmed outbreak. Scotland and Wales followed suit.
The European Union also reimposed a ban on British meat exports to the bloc's other member states, the European Commission said.
A spokesman for British Prime Minister Gordon Brown denied the government had given the all-clear too soon, telling reporters: "This was a decision that was made on the basis of scientific evidence."
His spokesman insisted there was "absolutely no truth" in any suggestion that Britain's chief veterinary officer Debby Reynolds had been pressured to lift restrictions.
Britain's red meat export market is worth about 500 million pounds (730 million euros, one billion dollars) a year, mostly with the EU. Britain was the ninth largest beef exporter last year among the 27-member bloc.
The outbreaks raised the spectre of a repeat of a 2001 crisis, in which up to 10 million animals were culled and which cost the national economy about eight billion pounds (11.7 billion euros, 16.0 billion dollars).
Brown on Thursday chaired a second meeting of COBRA, Britain's top emergency contingencies cabinet, which is coordinating the response to the outbreak.
Environment Secretary Hilary Benn said immunisation of livestock was being considered and said vaccines were ready if required.
The Soil Association, which campaigns for organic farming, urged the authorities to use vaccination to contain the outbreak.
"This must be a 'vaccinate to live' policy, rather than slaughtering perfectly healthy animals simply to serve the interests of a few large exporters," said the Soil Association's Phil Stocker.
Fears that the disease had spread further afield proved unfounded though after tests came back negative on a pig farm 150 miles away in Norfolk, eastern England, a spokesman for the agriculture ministry said late Thursday.
"All the tests have come back negative," a Defra spokesman told AFP. "The temporary control zone has been lifted." He said no animals were slaughtered there.