Tony Martin was living alone at his farmhouse in Emneth Hungate, Norfolk, nicknamed Bleak House, when he caught Brendon Fearon, then 29, and Fred Barras, 16, inside his house.
He fired his shotgun three times towards the intruders, killing Barras.
He was initially jailed for nine years after being convicted of murder but the conviction was reduced to manslaughter on appeal and his sentence was reduced to three years.
The case provoked a national debate about the measures homeowners can take to defend their property.
Speaking about the latest incident, Mr Martin, who no longer lives in Emneth Hungate, said he was visiting the shed when he saw the man attempting to steal car batteries.
– Tony Martin, Farmer
"There were weapons inside the shed so, if I had wanted to fight him off, I could have.
"I wished I had but, after everything I've been through in the past, I just couldn't face all that hassle again.
"It isn't the first time it's happened since I've been out of prison - it's happened two or three times.
"I haven't changed my views about what happened in 1999 but the whole experience has made me lose faith in the system and I didn't want to be made out as the criminal again."