Formerly assigned to Cetotherium

The following species were originally described as nominal species of Cetotherium but have been either reassigned to other genera or removed from Cetotherium:

• Cetotherium furlongi Kellogg, 1925,^[5] is known from a partial skull from the Burdigalian of the Vaqueros Formation in California, but the holotype is lost.^[6]
• Cetotherium gastaldii Strobel, 1875,^[7] known from the early Pliocene-age Sabbie d'Asti Formation of the Piedmont region in Italy, is now the type species of the eschrichtiid genus Eschrichtioides.^[8]
• Cetotherium klinderi Brandt, 1871,^[9] is known from an isolated earbone from Miocene sediments in Chişinău, Moldova. Although fragmentary, it is not congeneric with the two species of Cetotherium.^[3][10]
• Cetotherium maicopicum Spasski, 1951,^[11] based on a specimen from the late Miocene of the Russian Caucasus, was reassigned to the genus Kurdalagonus from the same region in 2012, although Gol'din and Startsev (2016) have questioned this referral.^[12][10]
• Cetotherium mayeri Brandt, 1871,^[9] known from a partial skeleton, has been reassigned to Mithridatocetus.^[3][10]

Cetotherium incertum Brandt, 1873, known from a vertebra, and "Ziphius" priscus Eichwald, 1840 are nomina dubia, while Cetotherium pusillum Nordmann, 1860 requires re-assessment.^[10]