Mr Lowry said he was concerned about his sheep but also his own safety.
"What happens when someone disturbs them while they are doing this? I'm sure they are not afraid to shoot someone," he said.
"This could turn into a homicide."
Mr Lowry said the farm was hit late at night.
Federated Farmers Rotorua provincial president Neil Heather, a sheep and beef farmer, said recent incidents of sheep rustling were concerning.
"It could be happening on a lot of farms and the farmers might not notice until it is time to count up."
He said there was a big black market for meat.
"The amount these people are taking, it has to be supplying someone who would be selling the meat."
Mr Heather said rustling happened all year round but the recent incidents on Mr Lowry's farm were especially concerning.
"It is worrying when firearms are involved, it means things have that much more potential to get out of hand."
Mr Heather said farmers or rural residents could help the situation by reporting suspicious vehicles.
"We expect a reasonable response from police but sometimes there is not enough information to give them."
Senior Sergeant Karl Konlechner of the Rotorua police said rustling wasn't reported to police often.
"We do get the odd report but they are usually after the fact.
"We do encourage people to contact us about these events as soon as they can by calling 111."
Taupo Senior Sergeant Greg Weston said the last issue with sheep poachers in the Taupo area was at a farm near the base of Mt Tauhara. He said a police dog handler took it upon himself to take an interest and was "Johnny on the spot" when security staff employed by the farmer spotted suspicious activity.
"It's definitely taken pretty seriously."
Mr Weston said it wasn't uncommon for farmers to employ security staff if they had concerns about rustling.
Bay of Plenty Federated Farmers meat and fibre chairman Rick Powdrell said Eastern Bay of Plenty farmers were starting to get annoyed with sheep thefts.
"A lot of farmers are starting to lock their gates - it's their livelihood at stake."
He said while often only a single sheep was taken, it was turning into a regular occurrence for some farmers.
Mr Powdrell said sheep rustling could have been connected with rising meat prices.
"People are just looking for an easy way out."
Senior Sergeant Mark van der Kley of the Kawerau police said that recently sheep had gone missing in Te Teko, Whakatane and Ruatoki. "You often find if there's a large social gathering, a few sheep will go missing."
Mr van der Kley said often people they caught, who had stolen only one or two sheep, would claim they were just trying to feed their family. But stealing sheep was still theft and carried a possible penalty of jail, he said.
- Additional reporting Rebecca Malcolm and Kristy Martin