Tuberculosis levels in cattle have risen in the original two areas of the country where the badger cull has been piloted over the past five years, raising questions about the merit of expanding the scheme.

The figures are confirmed in official data quietly released last week as the government announced plans to expand the controversial cull in England, which campaigners say could see more than 60,000 badgers killed this year.

The figures suggest that, following some early success in bringing the levels down, bovine TB is now on the rise in the zones, in Gloucestershire and Somerset.

Analysis by the vet and former government scientist Dr Iain McGill, who led calls for a public inquiry into the BSE scandal, reveals that the proportion of herds with bovine TB in the Gloucestershire pilot zone increased from 6.9% at the start of culling to 9% over the five-year period.

The rate of occurrence of new confirmed bovine TB cases – known as the incidence rate – was 13.2% last year, compared with 12.7% when the cull began in 2013.

In Somerset, the incidence rate declined, but the disease has become more widespread across herds. The official data shows that the proportion of herds with bovine TB increased from 6.1% when culling started to 6.7% at the end of last year. Defra chooses not to focus on the five-year data. Instead, it points to an earlier report that found a decline in bovine TB in the first two years of the cull.

“The government had all of the data but only released it simultaneous to the announcement on Wednesday of the massacre of up to 62,000 badgers,” said McGill, who has called for a public inquiry into the government’s handling of the cull.

The government has sanctioned the killing of more than 60,000 badgers this year. Photograph: Education Images/Universal Images Group via Getty Images

“That they could have tried to hide this data in order to justify such a massacre of protected wildlife, whilst referring glibly to data from 2015 in support of their case, is corrupt and criminal. Defra have manipulated and hidden scientific data to such a degree that it amounts to systemic scientific fraud.”

A Defra spokesman said: “Bovine TB remains one of the greatest animal health threats to the UK, causing devastation for hard-working farmers and rural communities.”

He pointed out that “detailed analysis on the effect of culling in the first two cull areas over the first two years showed a 58% reduction in the disease in cattle in the Gloucestershire badger control area and a 21% reduction in Somerset after two years of badger control compared with un-culled areas.”

The spokesman added: “There is no single measure that will provide an easy answer to beating the disease. That is why we are pursuing a range of interventions to eradicate the disease by 2038, including tighter cattle movement controls, regular testing and vaccinations.”

The government has licensed more than 40 culling zones across England. But Defra said it was too early for the other cull areas to show a drop in new cases of TB.

Caroline Lucas, the Green party MP, the Queen guitarist and animal rights activist Brian May, and the Badger Trust have joined calls for a public inquiry into the cull.