RSPCA inspectors had been investigating a 45-dog puppy farm in Loddon Shire since early last year, during a time when six dogs were surrendered to an animal shelter suffering a range of health conditions.

However the RSPCA said its Major Investigation Unit had inspected more than 100 dog and cat breeders in the past three years, and have prosecuted multiple businesses.

Related: Loddon Shire set to refuse permit to puppy farm, which has operated for years

The RSPCA said it has had limited enforcement powers in the past, but they were bolstered in April this year.

The puppy farm owner in Loddon Shire continued to sell the dogs on Facebook and The Trading Post, with ads still online today, despite not possessing a permit to operate the business. Posts on its Facebook page indicate the regular sale of cavaliers, pugs and pugaliers.

The Domestic Animals Act states a person “must not conduct a domestic animal business on a premises which is not registered for that purpose with the council”, a crime punishable by up to a $95,000 fine.

Loddon Shire voted against granting the business a permit at its Tuesday meeting.

Animal rights group Oscar’s Law founder Debra Tranter said the RSPCA had a “duty of care” to protect dogs being kept in puppy farms, and they must be seized.

“They’ve basically admitted they have sat back and allowed the public to purchase puppies from an illegal non-compliant puppy factory for almost a year,” she said.

“The government gave them a mandate and the resources to shut illegal puppy factories down, not just visit them whilst they carry on their illegal business.”

Ms Tranter said the RSPCA should be stripped of its enforcement powers, and an independent office of animal welfare should be established.

The RSPCA was given $5 million in 2015 to establish a Special Investigations Unit to “identify, deter and disrupt” illegal dog and cat breeding businesses.

The body is now known as the Major Investigations Unit, which also investigates greyhounds and horses, rather than just dog and cat breeders.

Ms Tranter said the switch from the SIU to the MIU went against the purpose of the $5 million state government funding, which should solely be used to investigate illegal dog and cat breeders.

The RSPCA faced calls to be stripped of its enforcement powers in 2016 after 20 dead horses were found on a Bulla property, two weeks after it was reported to the RSPCA.

Animal welfare lawyers demanded a new unit be established within Victoria Police, because the RSPCA appeared to not have the resources to undertake enforcement action.

RSPCA Victoria inspectorate team leader Lisa Calleja said they had been able to achieve prosecutions in recent years, including one against a dog breeder in the City of Ballarat. Their dogs were seized in February 2016, and the business owners were sentenced in December last year.

Ms Calleja said the MIU engages in disrupting illegal dog and cat breeders, their supply chains, “as well as helping with data collation and the rehabilitation and care of animals seized from these breeders”.

“RSPCA Victoria’s Major Investigations Unit has conduct more than 100 inspections of dog and cat breeding facilities and has assessed over 1000 animals,” she said.

Ms Calleja said new powers were brought in in April to increase the MIU’s power of enforcement.

“Historically, RSPCA Victoria’s Major Investigations Unit has had limited powers of enforcement under the DAA and our Inspectors have acted within those powers in regards to this matter,” she said.

“However, under the Domestic Animals Amendment (Puppy Farms and Pet Shops) Act 2017, as of 10 April 2018 the MIU’s powers of enforcement have increased, and RSPCA Victoria Inspectors are working alongside Loddon Shire Council in the ongoing investigation of this property.

“As this is an ongoing investigation, we are not in a position to comment further.”

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