The air pollution index in the capital Kuala Lumpur posted a reading of 77, edging towards the unhealthy range of 101-200, and several other locations were affected including Port Klang on the west coast with a reading of 78.
In the tourist destination of Malacca just south of the capital, the index rose to 81 and in parts of nearby Negeri Sembilan state towns recorded readings of up to 87.
Burning in Indonesia and some parts of Malaysia to clear land for crops causes an annual haze that afflicts Malaysia, Singapore and Thailand as well as Indonesia itself.
So far this year, Malaysia's worst-affected region has been the eastern states on Borneo island, particularly Sarawak where the capital Kuching had a reading of 157 last week.
However, heavy rain partly induced by cloudseeding washed away the acrid haze over the weekend and Kuching's air index had subsided to 65 on Tuesday.
In response to demands that it tackle the problem, Indonesia said Tuesday it will deploy hundreds of police and troops to fight fires raging on Sumatra island which is separated from peninsular Malaysia by only a narrow waterway.
The Indonesian government has outlawed land clearing by fire but weak enforcement means the ban is largely ignored.