The Badger Trust has blamed a rise in bovine tuberculosis on a threefold increase in tests on officially "TB-free" herds.
Latest figures from DEFRA showed that the number of cattle slaughtered in the UK due to bovine TB has risen by 12% in the past year.
From January to October last year, 31,146 cattle were slaughtered as reactors or direct contacts, compared to 27,788 during the same period in 2011.
The Badger Trust said the increase of 3,358 cattle slaughtered during this period coincided with a threefold increase in the number of tests on officially TB-free herds - 9,264.
These herds were hiding infection and were "clearly not TB-free, but were part of a continuing deep reservoir of infection in the cattle population", it added.
The trust has called for the rigorous application of new stricter cattle controls and nationwide annual testing of cattle. It said "officially TB-free" was clearly a "suspect designation".
A recent a recent study, which claimed that one in 10 Welsh livestock farmers had illegally killed badgers during the past year, was "evidence of wholesale law-breaking by Welsh farmers", the trust said in a statement.
This was further proof that farming industry organisations were unable to ensure their members obey the law, although they continue to demand massive privileges, the trust added.
In addition, the UK farming industry was facing "massive challenges" from international and industry authorities to address urgent issues such as mortality in youngstock and lameness in dairy cattle.
A report by the Cattle Health and Welfare Group (CHAWG) on the state of British farming, published last autumn, said mortality and lameness continued to be a problem and about 240,000 cattle die on farms each year from unknown causes - almost 10 times the number killed because of bovine TB.
"These revelations show the industry has much to do to set its farmyards in order instead of rushing to slaughter thousands of badgers for barely marginal advantage in the long-term," the Badger Trust said in a statement.
David Williams, chairman of the Badger Trust, said: "It would hardly be surprising that bovine tuberculosis was slowly spreading after an historic lack of controls."
He added: "Keynote reports amount to authoritative and independent support for the Badger Trust's conviction that the UK agricultural industry is ill-equipped to monitor its own affairs and to observe tuberculosis restrictions imposed in its own interests."
More on this topic
Bovine TB and the badger cull
Follow me on: Twitter
Philip Case on G+