Kriangkrai Namthaisong, a doctor at the ministry, on Wednesday urged children and pregnant women to stay indoors.
Anyone going outside should wear a high-quality N95 anti-pollution mask, he added.
During another pollution peak in late January and early February, city authorities urged people to work from home.
A spokesman for Bangkok governor Chadchart Sittipunt -- elected last year with promises to improve the city's environment -- said they would not hesitate to issue another similar order if the situation got worse.
Aekvarunyoo Amrapala told AFP that nurseries run by the city had set up special "no dust rooms" with air purifiers to protect young children, as well as checkpoints to monitor vehicle emissions.
The public health ministry said 50 districts in Bangkok on Wednesday recorded unsafe levels of the most dangerous PM2.5 particles -- so tiny they can enter the bloodstream -- while on Thursday they remained well above World Health Organization guidelines.
PM2.5 levels have been above safe limits for most of Bangkok for the past three days, according to the government's pollution control department.
The situation was worse in the northern city of Chiang Mai, in an agricultural region where farmers burn crop stubble at this time of year.
Around midday (0500 GMT), the popular tourist destination was ranked the third-most polluted city in the world by monitoring firm IQAir.