After the establishment of JMF, Sultan Abu Bakar decreed the creation of a flag for JMF as a symbol of identification, sovereignty, and to enhance its dignity.

The Commandant is the highest-ranking officer in the JMF organization. The Commandant's flag is blue with a small yellow square near the hoist, adorned with a red crescent and five-pointed star. Blue represents the King and the State, yellow symbolizes royalty, and red signifies courage. The crescent and star are symbols of the Islamic faith. At the bottom end of the flag, there is a symbol of a crossed sword and keris with the inscription "Timbalan Setia Negeri" in Jawi script. This symbol signifies Sultan Abu Bakar integrating Western and Eastern cultures and perspectives in governing the state. A crown is placed at the top of the emblem, signifying the King's leadership of JMF.

The flag is hoisted whenever the Commandant attends ceremonies at the JMF headquarters.

The JMF flag is similar to the design and colour of the flag of the Commandant, except the device at the fly contains only the crossed sword and keris. This flag is ceremoniously raised daily at the JMF Headquarters at dawn to the bugle tunes of “Reveille”, and lowered at dusk, accompanied by the “Last Post”.

Sultan Ibrahim conferred the banners on May 11, 1916, in a ceremony on Bukit Timbalan, commemorating the 30th anniversary of the establishment of the JMF.

The JMF banner is a blue flag with tassels. At the top of the flag is inscribed with "Allah Peliharakan" in Jawi script. The lower part contains a symbol of crossed swords and a keris, connected at the hilt with a crest that reads "Timbalan Setia Negeri" in Jawi script. A crown is placed at the top of the symbol, signifying "Allah Peliharakan Timbalan Setia Negeri." The original banner is kept at the JMF Headquarters.

Sultan Iskandar bestowed a new banner in a ceremony on August 20, 1986, at the Padang Istana Besar in conjunction with the celebration of the 100th anniversary of the establishment of JMF. A total of 180 officers and members of various ranks, led by Captain Dato’ Othman Daud as the Deputy State Officer, participated in the ceremony.

The JMF banner is carried by the Flag Officer and paraded during the honor guard procession in royal ceremonies, including the celebration of Tuanku's birthday, Tuanku's coronation ceremony, and the opening ceremony of the State Assembly session.

References:

1. Abdul Rahim Ramli's "History of Royal Customs and Traditions in Johor".
2. JMF.
3. The Johor Military Forces Enactment No 31, 1937.