The RSPCA is investigating after the Cartmill Centre, north of Brisbane, decided not to move the animals to a nearby holding area during Sunday night's heavy rains, saying it was too dangerous.

The decision was branded "disgusting" by one of more than a dozen locals who watched on as the waters rose and "not good enough" by the local councillor.

Water flooded through the Burpengary Riding for the Disabled Association facility as nearby Morayfield copped 134 millimetres in a downpour that drenched the south-east.

Burpengary Pony Club vice-president Warren Jensen, who was not speaking on behalf of the club, said he and several others tried to wade through chest-deep water to rescue the horses but it was too dangerous.

"The horses were standing in about a metre of water," he said.

"There was a gully between the horses and us.

"Myself and a couple of others waded out to up to our chest in bloody freezing cold water to try to get the horses but we had to turn around. That was about 9 o'clock."

The centre has a long history of flooding. One Burpengary resident refused to send back two horses after he found them floating down a creek following heavy rain last year, Caboolture News reported.

After flooding last year, Moreton Bay Council helped the organisation draft a disaster management plan and kicked in a small amount of funding to build a temporary shelter for horses on higher ground.

That plan included several staged responses, ranging from moving equipment to evacuating the horses themselves.

The council began issuing warnings to the centre about 4.30pm as a nearby creek rose but the direction to move the animals to the holding pen didn't come through until 6.44pm.

Burpengary RDA president Jane Sayer, who has been heavily criticised and faced calls for resignation in the wake of the incident, said by then it was too late.

"We had already made the decision that was the safest place for horses and there was only localised flooding," she said.

"It was impossible at that time to do it in a way that was safe and we made the decision about what we believed was the best way of dealing with it. It was safe.

"David, our very experienced volunteer who was dealing with the water, was monitoring it and it was dropping by some small amount (after peaking at 7.30pm)."

Ms Sayer said the horses never had more than 40 centimetres of water over their feet and accused the people on site on Sunday night of breaking into the facility and being abusive.

She said the organisation moved the horses to slightly higher ground earlier in the afternoon and took the decision not to risk lives to move the horses later in the evening.

Local councillor Adrian Raedel said the centre followed the disaster management plan two weeks earlier but failed to do so this time around.

"It's no longer good enough," he said.

"Just because they think that it's not going to flood, it's not good enough.

"They get the warnings. They need to follow the disaster management plan.

"This has proven that their gut feeling is not good enough."

RSPCA Qld Chief Inspector Daniel Young said horses had allegedly died in the property in the past and this was different to owners being "caught out by unexpected freak weather".

"It is concerning to hear that members of the public are potentially putting themselves at risk by entering floodwater to remove horses where the situation could have been avoided," he said in a statement on Monday.

"On this occasion numerous alerts were broadcast advising of the potential for flash flooding."