President Mutharika made the remarks in Mulanje during the launch of Malawi Rural Electrification Programme-MAREP Phase 8.
He said his government is implementing public infrastructure programmes such as constructing roads and water facilities in both towns and rural areas.
In these programmes, councils play a pivotal role in identifying projects and contractors and processing payment, following the Decentralisation Policy.
However, the councils have been making headlines for rampant abuse of funds, hence Mutharika's warning.
"Let me appeal to all councils. I want corruption to stop in the councils. You are awarding road contracts to people who are not qualified. Some councillors have personal businesses and you are taking roads contracts when you don't have experience. That has to stop. I am directing the Minister of Local Government to ensure that ACB should curb this malpractice at once," Mutharika said.
Mutharika emphasised that he will not protect anyone including members of his cabinet and party officials if they are found involved in corruption.