Southeasterly winds have blown smog from the fires, which regularly cause a haze that smothers Indonesia's neighbours, across the Malacca Strait to peninsular Malaysia, the meteorological department said.
Visbility at Kuala Lumpur International Airport was down from 10 kilometres (16 miles) to just four kilometers, and Senai airport in Johor state next to Singapore to 2.5 kilometers, officials said.
They said air traffic had not been affected so far.
Environmental department data Monday showed air quality at unhealthy levels in seven areas including central Pahang state.
In the tourist destination of Malacca, readings on the Air Pollutant Index hit 115 and several areas in Johor also registered unhealthy, a reading which fall in the range of 101-200 on the index.
In Singapore, the National Environment Agency said it was maintaining a weekend health advisory, urging people in general to avoid "vigorous outdoor activity" and the elderly and ill to be on particular guard.
Singapore's pollution index rose slightly early Monday to 88, although down from Saturday's unhealthy levels of 100-plus.
Indonesia's annual burn-off to clear land for agriculture causes a fog-like haze that also carries with it a burning smell.
The government has outlawed land-clearing by fire but its weak enforcement means the ban is largely ignored. Indonesia itself is also affected and some residents have resorted to praying for rain to alleviate the smog.
Environment ministers from Singapore, Malaysia and other regional nations met Friday in Indonesia to search for ways to combat the annual problem, which disrupts travel and leads to health problems.
The ministers told their hosts promptly to ratify a regional treaty aimed at preventing cross-border haze pollution.
Last week Indonesian President Susilo Bambang Yudhoyono apologized to both Singapore and Malaysia over the haze.