Experts have also warned there could be more torrential rain to follow.
Ms Cunningham said: "Once again we have seen the misery and destruction flooding can cause. Our thoughts are with those whose lives and livelihoods have been affected by the overnight floods. I have asked to be kept fully informed of developments and will be keeping in touch with the councils affected. I'd like to thank all those who have again responded so quickly and effectively to minimise the impact of the floods.
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"Climate change is clearly happening on our doorsteps and flooding events such as these are likely to occur with increasing frequency. Everyone needs to be aware of the increased risks and, as we have seen in the last 24 hours, that doesn't just apply to those living in areas where there is a history of flooding."
Floods up to 5ft deep damaged homes and businesses on Sunday. The worst hit areas were Huntly and Aberdeenshire.
Ms Cunningham continued: "Through SEPA we are continuing to invest in flood awareness and flood warning schemes to try and minimise the impact flooding has on families and businesses. I launched the latest SEPA awareness campaign only last Friday.
"We also need to take radical steps to tackle our carbon emission levels and to ensure communities get the protection they need, which is why we have recently pushed far-reaching climate change and flooding legislation through Parliament."
(CD/BMcC)
