Using his Twitter account, the News Corporation chairman claimed the attacks on Brooks were unfair.
The 80-year-old wrote: “Now they are complaining about R Brooks saving an old horse from the glue factory!”
Follower Paul Blandford replied with the jibe: “Of all the things you could be called rupert, an ‘old horse’ is by far the most flattering…!”
MP Tom Watson, who has been at the forefront of the campaign against phone hacking and other wrongdoing, tweeted back, saying “@rupertmurdoch You comment on her horse but not on her insider knowledge of a criminal investigation into your company. Have you no shame?”
The Metropolitan Police admitted they had loaned Brooks the horse, which had reached the end of its working life, to keep at her home in Chipping Norton, Oxfordshire.
The Met added in a statement: “”When a police horse reaches the end of its working life, Mounted Branch officers find it a suitable retirement home … the appropriate welfare checks are carried out by Mounted Branch officers.
“Whilst responsibility for feeding the animal and paying vet bills passes to the person entrusted with 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 MPS at any time.”
Brooks was one of just 12 people allowed to take ex-police horses home.
A Met spokesman said Brooks returned the horse, named Raisa, in “poor” condition.
Raisa was re-homed with a police officer in 2010 and later died of natural causes.