This follows a spike in Covid-19 cases there, senior minister for security Ismail Sabri Yaakob said today.
In Penang, a total of 13 localities in Bayan Lepas will be placed under EMCO.
The localities are: Sri Bayu, Bayu Tiara, Bayu Nyaman, Halaman Murni, Bayan Permai, Bayan Tiara, Taman Ara Indah, Kampung Bukit, Kampung Perlis, Kampung Masjid, Jalan Mahkamah, Jalan Kampung Pak Lah and Lebuh Kampung Bukit.
Ismail said the localities had recorded 83 positive cases recently.
In Pahang, four residential areas in Bentong will be placed under EMCO after 19 cases were recorded in the areas.
The residential areas are: Taman Bentong Makmur, Taman Harmoni, Taman Kolej and Taman Desa Damai.
In Sabah, Lorong Taman Utama 5, 6, 7 and 8, Taman Utama in Sandakan, will also be placed under EMCO after nine positive cases were detected from the 13 people screened.
Kampung Sepagaya Hulu, Silamin in Lahad Datu, will be placed under EMCO after 19 positive cases were recorded during the screening of 35 people.
Two localities in Kota Kinabalu, namely Rumah Murah Kepayan and Kampung Tanjung Aru Baru will be placed under EMCO after 24 cases were recorded in the localities.
Meanwhile, Ismail announced that the EMCO at Pekan subdistrict, Sabah will be extended to 15 new localities.
The localities are: Bajau Laut-Palauh, Kampung Cina, Kampung Selamat, Kampung Kunak Jaya, Kampung Singgah Mata, Kampung Kunak Kecil, Kampung Bagiang, Kampung Jaya Baru, Kampung Datuk Haji Zainal Gunong, Kampung JKR Lama, Kampung Haji Mohd Noor, Kampung Pangkalan Lama, Kampung Pangkalan Laut, Kampung Sungai Atas and Pekan Kunak.
The EMCO at SMU Pantai Manis, Papar in Sabah will also be extended until June 17.
However, the EMCO at UTM Skudai in Johor will end tomorrow as scheduled while at Gugusan Mendi, Bera, Pahang, it will end today, one day earlier than scheduled.
The minister also said police arrested 792 people yesterday for MCO-related offences, with 781 issued compound fines, 10 remanded and one freed on bail.
The offences included failing to observe physical distancing (180), failing to wear face masks (170), failing to register personal details prior to entering premises (135), crossing state or district lines without permission (102), flouting movement restrictions (88), carrying more than the passenger limit (88), and others (20).
Ismail said police also arrested 10 illegal immigrants and seized seven vehicles under the ongoing Op Benteng.