The latest find comes a few weeks after another police operation turned up 1.2 tonnes of crystal meth.
Nearly 600kg (1,300lbs) of mostly crystal meth was found over the weekend, most of it in a container truck in the northern state of Perak, police said.
The seizures come a month after police got a record bust of 1.2 tonnes of crystal meth, known locally as shabu, disguised as tea in a shipment from Myanmar.
Malaysian police chief Mohamad Fuzi Harun said: "We found 569.5 kg of what we believe is shabu in the container, valued at 28.47 million ringgit (£5.4m)."
Officers believe the container was on the way to Port Klang, where it would have been split between local distribution and export.
Three men aged between 39 and 49 were arrested in three locations in Perak.
They have been remanded in custody until 19 January as the investigation continues.
Malaysia's Sun Daily reports that five men were arrested in a separate operation, as police took down a syndicate supplying drugs to inmates in a prison.
It said 16.4kg (36lbs) of heroin, 9.88kg (22lbs) of shabu and 940 ecstasy pills were seized.