Kuala Lumpur residents wore face masks as protection from the choking smog, while visibility was low.
Nine out of some 50 measuring stations recorded air pollutant index readings above 100, which signify "unhealthy" air quality.
Readings in Sibu town in Sarawak state on Borneo breached 200 -- designated as "very unhealthy" -- on Monday, but recovered slightly early Tuesday.
A reading of above 300 signifies "hazardous" air.
Readings hit 750 in a town in southern Malaysia in June last year, the highest seen in the Southeast Asian country for 16 years, causing a declaration of emergency in several districts, school closures and a regional diplomatic row.
Haze is an annual problem during drier summer months when monsoon winds blow smoke from fires mostly on the huge Indonesian island of Sumatra, which lies across the Malacca Strait from Malaysia and Singapore.
The fires have been largely blamed on palm oil firms using the illegal but cheap method of burning vast tracts of rainforest and peatland to clear them for planting.
Indonesian authorities had warned last month that Malaysia and Singapore could be hit by haze again after a huge jump in forest fires in Riau province on Sumatra, which was at the centre of the air pollution crisis last year.
Malaysia -- usually known for its tropical heavy downpours -- this year has also been plagued by drought, leading to water rationing, particularly in the central state of Selangor, the country's economic hub, which surrounds the capital.