THIEVES pinched almost $27,000 worth of sheep from North East Water's Wangaratta and Benalla treatment plants last year.

Increased security including CCTV cameras have been installed and more regular flock counts at the water authority's farms have begun in a bid to deter thieves.

Labor's opposition water spokesman John Lenders today said FOI documents showed a count on March 21, 2011 revealed 69 sheep disappeared from the Wangaratta Wastewater Treatment Plant and another 137 sheep were missing from the Benalla site on June 30.

"Water Minister Peter Walsh failed to maintain the security of hundreds of sheep at the plants and taxpayers are footing the bill for the losses," Mr Lenders said.

He said the documents revealed Mr Walsh reported the incidents to Finance Minister Robert Clarke and stated to stop losses the sheep would be counted more often.

North East Water managing director Craig Heiner said the water authority's farming operation at its Benalla and Wangaratta sites had been targets during a spate of livestock thefts across the state.

He said almost $26,000 worth of sheep and two quad bikes - the latest stolen only a couple of weeks ago from a Wangaratta shed - had been taken.

Mr Heiner said in a typical year the authority made $100,000 on its sheep operation.

"In that year we made $130-$140,000 from sheep trading but that would have been greater if the sheep were not taken," Mr Heiner said. 

Quarterly counts of the flock have been changed to monthly counts to keep on top of numbers, he said.

He said the thefts were reported to police and the latest theft of a $13,000 Honda red bike was captured on security camera.

Mr Walsh said in a statement this afternoon Wangaratta and Benalla police investigated the sheep thefts.

"There was an increase in the number of sheep recorded stolen in Victoria from 2009/2010 to 2010/2011, likely due to record prices for sheep, lamb and wool.

"As part of the implementation our election policy the Victorian Coalition Government announced in October a new Livestock and Farm Crime Specialists Group within Victoria Police. The Benalla region will be one of its focus areas.

"The Livestock and Farm Crime Specialists Group was established to investigate the spike in livestock theft, particularly sheep, and undertake targeted operations, prosecute offenders and roll out crime prevention initiatives."