The man was identified as Samsul Sangunim, who was taken hostage in Gaya Island, Semporna, Malaysia, on September 11, 2018, along with another Indonesian Usman Yunus.
Yunus managed to escape on Dec 5 and had been reunited with his family in Indonesia.
"Since the first incident of hostage-taking of Indonesians in 2016, such kind of video had often been sent by the kidnappers," the ministry`s Director for Indonesian Protection, Lalu Muhammad Iqbal, noted in a short message here on Saturday.
In the 10-second video, Sangunim, in pink short pants, is seen crying while yelling out, "help me, boss, help me, boss, help."
Sangunim was seen kneeling in a newly dug hole, while at the back, two men were pointing long-barrel rifles at him.
According to sources in the Philippines, the video was sent by the Abu Sayyaf group to the owner of the fishing ship to demand ransom for Sangunim`s release.
Sangunim was captured along with a Malaysian and two Indonesians in a fishing boat in the waters near the Philippines` Tawi Tawi island chain.
Most negotiations to release the hostages were believed to be made directly with families or the ship owners.
According to media reports in the Philippines, Abu Sayyaf demanded 4 million peso (some Rp1 billion) of ransom for the release of Yunus and Sangunim.
They were allegedly kidnapped by Hatib Sawadjan and Indang Susukan.
Responding to the video, Iqbal reiterated that the Indonesian government had continued its attempts to free three Indonesians still held hostage in the Southern Philippines.
"During the process, the safety of hostages has always become our main concern," Iqbal noted.
Since 2016, a total of 36 Indonesians, mostly ship crews, were taken hostages in Southern Philippines.
Some 33 of them had been freed, while three others are still held hostage.
Reporting by Yashinta Difa Pramudyani