"The pollution is caused mainly by the open burning on Sumatra, Indonesia," a meteorological department spokesman told AFP on condition of anonymity.
The official said there were 442 "hotspots" or burning areas on Sumatra island on Thursday.
Visibility in central Pahang state dropped to 1.4 kilometres (0.9 miles) in some areas and 1.5 kilometres in southern Johor state but improved, while in the capital of eastern Sarawak, Kuching on Borneo island, it was 4 kilometres.
Some areas including the capital Kuala Lumpur where the 88-storey Petronas Twin Towers is situated and surrounding areas, saw visibility down to seven kilometres.
Normal visibility in Malaysia would be over 10 kilometres, the official said.
Malaysia in June declared that air pollution figures would remain a state secret due to fears the economy would be hurt by revealing how much smog from neighbouring Indonesia had blanketed parts of the country.
The pollution index measures the quality of air on a scale of zero to 300. It considers zero to 50 as good, 51 to 100 as moderate, 101 to 200 as unhealthy and 201 to 300 as very unhealthy. Anything above 300 is hazardous.
"Generally, the air quality level in Malaysia is "moderate," the environment department's director-general Rosenani Ibrahim told AFP. "The situation is unlikely to deteriorate with some expected showers on the way," she said.
Parts of Indonesia were on Wednesday enveloped in one of the worst days of haze this year, prompting residents to don face masks to ward off thick, choking fumes.
The haze, caused by forest and ground fires across Indonesia, descended on the province of South Kalimantan on Borneo island, reducing visibility and filling the air with a noxious burning smell.
In 1997 and 1998, choking haze caused by forest fires in Indonesia enveloped parts of Southeast Asia for months, causing serious health problems and traffic hazards and disrupting airline schedules.
The haze then caused an estimated 9.3 billion dollars in economic losses.