The government in mid-January had initially implemented a three-month ban on bauxite mining in the rural state of Pahang over concerns about hazardous dust and pollution.
"It is important for us to safeguard the environment," Environment Minister Wan Junaidi Tuanku Jaafar was quoted as saying by state news agency Bernama.
The additional three months will provide time to clear the more than 3.5 million tonnes of stockpiles, local media said.
AFP reported on the modern day gold rush of bauxite mining in Pahang and its impact on residents and the environment weeks before authorities announced the January ban.
Red dust was swirling around the pits and along the roads on which bauxite-laden trucks rumbled towards Kuantan, the capital of Pahang, for shipment to China.
Residents complained to AFP of a rise in respiratory problems and skin rashes.
Sea waters around Kuantan had turned red from contamination, worrying residents and environmentalists.
Demand for bauxite, which is used in aluminium production, is soaring -- fuelled by heavy demand from China.
Bauxite mining took off in Malaysia -- most of it illegal -- shortly after Indonesia, a top producer, banned mineral ore exports in January 2014 to encourage domestic metals processing, leaving major consumers in a supply crunch.
Malaysian bauxite output more than quadrupled year-on-year in 2014 to nearly 963,000 tonnes, according to government figures.