The warning has come from researchers at Queen's University, Belfast, who carried out the first study into the effects of illegal badger persecution.
About 5% of setts in Northern Ireland had recent signs of illegal damage.
The study found that this practice "contributed significantly to new bovine TB breakdowns in nearby cattle".
Bovine TB affects about 6% of cattle herds in Northern Ireland and there has been a long, controversial debate about the extent to which the disease is linked to badgers, which share a similar strain.
Dr David Wright, who led the study said: "Whilst interference with badger setts was relatively rare, it was clustered in known bovine TB hotspots in cattle and we hypothesised that those taking action against badgers may actually contribute to maintaining the disease.
"So we were interested in investigating the interaction of cattle and badgers in disturbed and undisturbed populations."
The study found the risk of bovine TB was "significantly elevated" in areas with dense badger populations and also in areas where there was high rates of sett interference, which has led to a degree of uncertainty over the findings.
QUB's Dr Neil Reid, who lectures in conservation biology, said: "The relationship between badger persecution and bovine TB in cattle could either be because persecuting badgers perturbs the population stimulating spread of the disease or farmers are more likely to persecute badgers if their livestock have previously had a TB breakdown.
"We can't say which way round the relationship is but we can say that persecuting badgers certainly does not lower TB risk in cattle, it is illegal and may make the situation worse.
"Farmers should be aware of the risks incurred by disturbing badger setts," he added.
The study found a number of sett entrances blocked with soil, boulders and branches, while some were pumped full of slurry.
Other setts had been inadvertently damaged by ploughing, livestock trampling or construction work.
Researchers also found evidence of digging around setts, which they said was "indicative of badger baiting".
The research was carried out by QUB's Institute for Global Food Security, in collaboration with the University of Glasgow and the Agri-Food and Biosciences Institute.
The study was funded by the Wellcome Trust and published in the journal, Nature Scientific Reports.
Farmers have been warned that damaging badger setts does not reduce the risk of bovine tuberculosis (TB) in cattle and could make the problem worse.