Background

Language Family: Austronesian / Malayo-Polynesian / Western Malayo-Polynesian / Borneo / Barito / East / Malagasy

Phonology

Pre-nasalized stops are proposed by O’Neill (2015) as being allophones of their oral counterparts brought about through nasal assimilation (p. 38). That being said, it’s widely documented that Malagasy doesn’t allow for consonant clusters (see Syllable Structure). Therefore, if such stops were treated as allophones, the underlying transcription would violate that very restriction. Based on this and on the fact that Rasoloson and Rubino (2005) include pre-nasalized stops as part of the phonemic inventory (p. 459), I will too.
Although the pre-nasalized /ɡ/ occurs in Malagasy, /ŋ/ is not attributed as being part of the official language (Rasoloson and Rubino 2005, 459). It is, however, said to be realized through nasal assimilation in the official language and part of the phonemic inventories in other dialects (e.g. Betsimisaraka) (O’Neill 2015, 13).
Geminate consonant do not occur in the language (Rasoloson and Rubino 2005, 460).

	Place of Articulation
Manner of Articulation	Labial	Dental	Alveolar	Velar	Glottal
Stops (plain)	p b	t̪ d̪	ts dz	k ɡ
Stops (prenasalized)	ᵐp ᵐb	ⁿt̪ ⁿd̪	ⁿts ⁿdz	ᵑk ᵑɡ
Affricates (trilled)			tʳ dʳ
Affricates (prenasalized and trilled)			ⁿtʳ ⁿdʳ
Fricatives	f v		s z		h
Nasals	m		n
Trills			r
Approximants			l
Note: For phonemes that share a cell, those on the left are voiceless and those on the right are voiced.

There is some controversy around the phoneme /o/. Although it appears to occur as a dialectal variant (e.g. Betsimisaraka) (O’Neill 2015, 13, 43), it is not attested as being part of the official inventory. Rather, authors argue that it’s phonetically realized as a result of reduced vowel duration (Rasoloson and Rubino 2005, 460), or as a result of /u/ being in environments with non-high vowels (O’Neill 2015, 42, 43).
There is a lack of consensus regarding the diphthongs of Malagasy (O’Neill 2015, 43–45). Therefore, I won’t account for them. However, it is important to note that some vowel sequences are actually realized on the surface as monophthongs (e.g. /ia/ and /ai/ as [e], and /ua/ as [o]) (Rasoloson and Rubino 2005, 460).

The Malagasy alphabet is referred to as the Abidy (Griffiths 1854, 11).
⟨ô⟩ is used for the sound [o] in loanwords (Rasoloson and Rubino 2005, 460).
Stress is denoted by accented vowels; however, we do not account for stress, so accented vowels will be transcribed to their plain representations.

Syllables in Malagasy follow a (C)V structure - codas are prohibited (Rasoloson and Rubino 2005, 460).
Aside from the consonants that appear in succession with the digraphs and trigraphs, no consonant clusters are allowed in syllable onsets (loanwords are exempt) (Rasoloson and Rubino 2005, 460).

Fricatives become stops in possessive and verbal constructions, reduplication, and compounding (Rasoloson and Rubino 2005, 461–62).
Pre-nasalized stops occur word-medially. Word-initially, the nasal is unpronounced and the oral stop is voiceless (Rasoloson and Rubino 2005, 459).
All velar stops palatalize following a vowel (Rasoloson and Rubino 2005, 459).
Vowels often become nasalized when preceding nasal or pre-nasalized consonants (Rasoloson and Rubino 2005, 460).
Vowels are often elided word-finally and intervocalically (Tench 2008, 2).

Griffiths, David. 1854. A Grammar of the Malagasy Language, in the Ankova Dialect.

O’Neill, Timothy. 2015. “The Phonology of Betsimisaraka Malagasy.” PhD thesis, University of Delaware.

Rasoloson, Janie, and Carl Rubino. 2005. “Malagasy.” In The Austronesian Languages of Asia and Madagascar. Psychology Press.

Tench, Paul. 2008. “Malagasy Interlanguage Phonology.” Cardiff University.