Muslim-majority Malaysia is a staunch supporter of the Palestinian cause and does not maintain diplomatic relations with Israel.
Anwar said on Tuesday that the government was looking into potential security risks arising from the use of Waze, which he said "was bound to Israeli laws."
"We cannot compromise on the security of people's data and identities," he said in a Facebook post after chairing a national cybersecurity committee meeting.
Anwar did not provide any details of the risks but recommended the use of TuJu, a domestic mapping app developed by the Malaysian Highway Authority, as an alternative.
Malaysia's Chief Secretary to the Government Shamsul Azri Abu Bakar said all civil servants would now be barred from using Waze, according to a letter dated Tuesday and addressed to the heads of government agencies.
The letter, reviewed by Reuters, said the directive followed a decision taken at the meeting chaired by Anwar, with the prohibition to take effect immediately.
An official with the Prime Minister's Department confirmed the letter's authenticity.
Waze, which was founded in Israel, uses satellite signals and crowd-sourced data from drivers to offer real-time traffic information. It was acquired by Alphabet-owned Google in 2013 for about $1 billion.
(Reporting by Rozanna Latiff; Editing by David Stanway)

(L-R) Myanmar Ambassador to the Philippines Ei Ei Tin, Royal Thailand Police Major General Apimook Karntayakorn, Timor Leste Interior Minister Francisco da Costa Guterres, Vietnam Ministry of Public Security Deputy Director Nguyen Minh Hieu, South Korea Incheon Chief Prosecutor Park Seong-min, Japan Deputy Commissioner General of National Police Agency Koichi Tachikawa, Philippine Department of Interior and Local Government Secretary Juanito Remulla, China Assistant Minister of Public Security Wuqin Lyu, Singapore Deputy Home Secretary Ngiam Shih Chun, Brunei Security and Law Minister Dato Seri Setia Awang Haji Sufian bin Haji Sabtu, Lao Ministry of Public Security Major General Kongsavat Bounlieng, Malaysia Home Minister Datuk Seri Saifuddin Nasution bin Ismail and ASEAN Deputy Secretary General Dato Astanah Abdul Aziz pose for pictures during the 16th Association of Southeast Asian Nations (ASEAN) Ministerial Meeting on Transnational Crime (AMMTC) + 3 Consulation at the Fairmont Hotel in Makati City, Metro Manila, Philippines, 21 October 2026. ASEAN ministers convened for a second day of meetings alongside partners from China, Japan, and South Korea. EPA/ROLEX DELA PENA
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