In 1918, a deadly influenza epidemic struck Western Samoa, killing one-fifth of the population on both Upolu and Savaiʻi.

Poyer was highly popular, and the Samoan people overwhelmingly wanted him to remain in office when his term ended.

[4][5] On March 1, 1915, Poyer relieved Lieutenant Charles Armijo Woodruff and became the twelfth Governor of American Samoa, the eleventh man to hold the office.

During the 1918 flu pandemic, Poyer quarantined American Samoa after hearing news reports of worldwide deaths on the radio.

Poyer transferred command of American Samoa to Warren Jay Terhune on June 10, 1919, ending his governorship.

The President of the United States of America takes pleasure in presenting the Navy Cross to Commander John Martin Poyer, United States Navy, for exceptionally meritorious service in a duty of great responsibility as Governor of American Samoa, for wise and successful administration of his office and especially for the extraordinarily successful measures by which American Samoa was kept absolutely immune from the epidemic of influenza at a time when in the neighboring islands of the Samoan group more than 10,000 deaths occurred, and when the percentage of deaths throughout the Polynesian Islands as a group, is reported to have ranged from 30 to 40 per cent of the population[10]