1. Indonesia

With 742 languages, Indonesia is ranked second in the world (after Papua New Guinea) and is the country with the most languages in Southeast Asia.

Indonesian is part of the Western Malayo-Polynesian subgroup, a branch of the Austronesian languages. According to Ethnologue, Indonesian was formed after Riau Malay, an old form of Malay originally spoken in Northeastern Sumatra.

Indonesian (Bahasa Indonesia) is Indonesia’s official language and the most widely spoken Malay language in the world.

2. The Philippines

Depending on the classifications, there are 120 to 187 languages in use in the Philippines (in Ethnologue: the language of the world, there are 180 languages).

Almost all are Malayo-Polynesian languages native to the archipelago. A number of Spanish-influenced creole varieties generally called Chavacano are also spoken in certain communities.

Tagalog and Cebuano are the most commonly spoken native languages, together comprising about half of the population of the Philippines. Filipino is a standardized version of Tagalog, spoken mainly in Metro Manila.

3. Malaysia

According to the data table of Ethnologue: the language of the world, Malaysia ranks 13th in the list of 20 countries with the most languages with 147 languages.

The indigenous languages of Malaysia belong to the Mon-Khmer and Malayo-Polynesian families. The national, or official, language is Malay which is the mother tongue of the majority Malay ethnic group. 

The government provides schooling at the primary level in each of the three major languages, Malay, Mandarin and Tamil. Within Malay and Tamil there are a number of dialectal differences. There are a number of Chinese languages native to the ethnic Chinese who originated from southern China, which include Yue, Min and Hakka Chinese.

According to seasia.co AND Wikipedia.

(https://seasia.co/2022/01/25/indonesia-ranks-2-on-countries-with-the-most-languages-here-s-the-complete-list-list AND Wikipedia)