The fires, concentrated on the islands of Borneo and Sumatra, are a regular occurence in the dry season, but appear to have worsened this year with more fires on highly-flammable peatland and amid a hot spell before the start of rains due this month.
In the town of Palangkaraya, in Indonesia's Central Kalimantan province on Borneo, visibility was extremely poor.
Cars used headlights to avoid accidents, while flights were delayed by four to five hours at the town's airport of Cilik Riwut.
The Antara state news agency said the air pollution index in the town was at a "dangerous" level and people were having to wear protective masks even in their homes.
Meanwhile, fires were also still raging in the Sebangau National Park in the province.
A task force of Indonesian officials arrived in Kalimantan on Sunday to assess the situation.
Purwasto, head of forest fire control at Indonesia's environment ministry, said on his way to Palangkaraya that the team would look at the situation for one or two days.
In Sumatra, haze stopped boats, carrying food staples to remote parts of the province, from navigating the Musi river with visibility cut to 200m.
In Malaysia, several areas in southern Johor state near Singapore were still recording unhealthy pollution levels on Sunday, while the situation in other areas was better.
Thailand also reported light smoke in southern parts of the country, and the governnment-run Thai News Agency said masks were given to people in Satun province.
Thick haze blowing across from Sumatra prompted Singapore to post a health advisory message on Saturday, warning people to scale back vigorous outdoor activity.
The situation improved in Singapore on Sunday, with the three-hour average Pollutant Standards Index down as low as 27, after hitting a nine-year high of 150 on Saturday.
A spokeswoman for the National Environment Agency said that south-southeasterly winds had blown some of the haze away from Singapore, but said that it could only be a temporary shift.
She said: "We expect that later in the afternoon it could shift in a south-southwesterly direction again."