| Flag | Date | Use | Description |
| 1871 onwards | Flag of the state of Johor | A blue field with an arranged crescent and five-pointed stars in a red canton. |
| 1912 onwards | Flag of the state of Kedah | A red field with the state coat of arms in the canton. |
| 1923 onwards | Flag of the state of Kelantan | A red field defaced with a white crescent and star and two white kris and spears. |
| 1957 onwards | Flag of the state of Malacca | Two equal bands of red and white, with a crescent and five-pointed star in a blue canton. |
| 1895 onwards | Flag of the state of Negeri Sembilan | A yellow field with two diagonal bands of red and black in the canton. |
| 1903 onwards | Flag of the state of Pahang | Two equal horizontal bands of white and black. |
| 1965 onwards | Flag of the state of Penang | A blue, white and yellow vertical tri-colour defaced with a betel nut tree. |
| 1879 onwards | Flag of the state of Perak | A white, yellow and black horizontal tri-colour. |
| 1870 onwards | Flag of the state of Perlis | Two equal horizontal bands of yellow and blue. |
| 1988 onwards | Flag of the state of Sabah | A blue, white, and red tri-colour, with the silhouette of Mount Kinabalu on a light blue canton. |
| 1988 onwards | Flag of the state of Sarawak | A yellow field with two diagonal bands of red and black, defaced with a nine-pointed star. |
| 1965 onwards | Flag of the state of Selangor | Red and yellow quartered, with a white crescent and five-pointed stars in the canton. |
| 1953 onwards | Flag of the state of Terengganu | A black field defaced with a white crescent and five-pointed star, with white at the edge. |
| Flag | Date | Use | Description |
| 2006 onwards | Flag of the Federal Territories | Three equal horizontal bands of yellow, blue, and red with the Malaysian coat of arms in the blue band. |
| 1990 onwards | Flag of Kuala Lumpur | Three equal bands of white, blue and white with three equal horizontal stripes of red on both white bands. There is a yellow crescent and yellow fourteen-pointed stars on the left within the blue band. Before 2006, this flag was used to represent the entire Federal Territories. |
| 1992 onwards | Flag of Labuan | Three equal horizontal bands of red, white, and blue, there is a yellow crescent and yellow fourteen-pointed stars in the white band. |
| 2001 onwards | Flag of Putrajaya | Three vertical bands of blue, yellow, and blue with the Malaysian coat of arms in the yellow band. |