Brooks was given a retired police horse to ride at her country house, police said on Tuesday.
Murdoch, 80, tweeted: "Now they are complaining about R Brooks saving an old horse from the glue factory!"
MP Tom Watson, who has been campaigning hard over the phone-hacking scandal, tweeted in response: "... You comment on her horse but not on her insider knowledge of a criminal investigation into your company. Have you no shame?"
However, had Murdoch done his research into the fate of retired police horses, he would have known that a glue factory certainly does not feature.
Horses with London's Metropolitan police are given good retirements in an acknowledgement of their faithful service. Many end up in the care of The Horse Trust, in Buckinghamshire.
The loaning of the horse, named Raisa, is the latest twist in the inquiry into phone-hacking by British journalists and links between the police and media.
Brooks, who rose to become chief executive of News International, the British newspaper subsidiary of News Corp, was given the retired police horse in 2008 to ride at her country house, police said on Tuesday.
Brooks, who is known to be a keen rider and is married to a racehorse trainer, cared for Raisa from 2008 to 2010.
She resigned last July amid mounting revelations about phone-hacking at a state-ordered inquiry into the illegal practice.
The Metropolitan Police chief Paul Stephenson has also resigned, amid growing numbers of questions over how close ties were between media executives and senior police.
A Metropolitan police spokesman said: "When a police horse reaches the end of its working life, mounted branch officers find it a suitable retirement home.
"Whilst responsibility for feeding the animal and paying vet bills passes to the person entrusted to its care at its new home, the horse remains the property of the Metropolitan Police Service.
"Retired police horses are not sold on and can be returned to the care of the Metropolitan Police at any time."
It was understood a total of 12 retired police horses were loaned out in such circumstances in 2008.
A further 29 had their duties ended between 2009 and 2011.