[2] During 1959, the botanical collection was transferred to the new Western Australian Herbarium and the museum and the art gallery became separate institutions.

The museum focussed its collecting and research interests in the areas of natural sciences, anthropology, archaeology, and Western Australia's history.

In February 2008, the Government of Western Australia announced that it would build a new A$500-million museum at the East Perth Power Station site.

[3] However, following the election of a new State Liberal party government under Colin Barnett, the redevelopment plans were scrapped in early February 2009.

[12] The Perth site also included the Discovery Centre, designed to help children and adults interact and learn about the museum's collections and research.

The museum is located in the historically significant Maritime Heritage Precinct, which includes the entrance to Fremantle Inner Harbour and associated installations; Forrest Landing - named after the pilot boat Lady Forrest which is also displayed inside the museum, the remnant of the original limestone bar used by Aboriginal men as a crossing point at the mouth of the Swan River; the migrant Welcome Walls memorial; and the World War II submarine slipway area.

Its staff members are involved in developing artefact management and cataloguing strategies, outreach and wreck-access programs, site-inspection techniques, and studies of diverse maritime sites, such as iron ship archaeology, characterised by its SS Xantho program and underwater aviation archaeology.

[22] Refurbished in July 2010, the Museum of the Great Southern is situated at the site of the first European settlement in Western Australia, in Albany.

This museum explores the region's biodiversity, the stories of the indigenous Noongar people and ancient natural environment.

[23] The museum was the original residence of Major Edmund Lockyer, the commanding officer of the settlement group that landed in Princess Royal Harbour on 26 December 1826, and formally proclaimed sovereignty on 21 January 1827 for King George IV of Great Britain, naming the place King George's Sound settlement (later renamed Frederickstown and then renamed again Albany).

[citation needed] The Museum of Geraldton is situated in Western Australia's rapidly growing mid-west region.

This museum explores the region's biodiversity, mining and agricultural history, the stories of the indigenous Yamaji people and the Dutch shipwrecks.

[31] In December 2020 the Western Australian Museum removed what it said were two factual errors on labels in a multimedia display after complaints about their veracity, including from the consul general of the People's Republic of China (PRC) in Perth.

"[36] The museum altered the visuals in response to the complaints, saying that the World Health Organization is still investigating the origin of COVID-19, and that the map "did not include Taiwan ... as part of China, which is not in line with Australian government policy".

"[32] Additionally, Mark Harrison, a senior lecturer in Chinese studies at the University of Tasmania, pointed out that contrary to the museum's claims, including Taiwan as part of China is "not actually reflective of 'Australian government policy'".

[38] The changes drew a critical reaction from Human Rights Watch researcher Sophie McNeill,[35] who said that it is "very important that our cultural institutions rely on accuracy and facts and don't bow to pressure from the Chinese Communist Party who are often trying to censor and rewrite history".