According to Malaysian daily, the New Straits Times, Mr Abdul Ghani Othman said the floods were due to the narrowing of the Johor River mouth caused by reclamation on Singapore's Tekong island located opposite the waterway.
He said the river burst its banks after excess rain water could not flow out to the sea fast enough.
Speaking to reporters on Wednesday, Malaysian Deputy Prime Minister Najib Razak, however, said it was too early to tell if the flooding was linked to the reclamation.
"There are all sorts of allegations but we can't come to a conclusion unless a thorough technical study is done on the cause of Johor's floods. The real cause is the exceptionally heavy rainfall," he said.
A spokesperson from Singapore's Ministry of National Development says these comments are unfounded and this is confirmed by the results from technical studies that were commissioned separately by both Malaysia and Singapore.
(Thanks Mr Big)