Airline officials said they are concerned about passenger weight because its fleet consists of small propeller planes that seat between three and 10 passengers, The Wall Street Journal reported Wednesday.
World Health Organization data indicates 55 percent of Samoans over the age of 20 are obese, meaning a severely overweight passenger could reduce a plane's capacity and threaten revenue.
"It's a pay-by-weight system and it's here to stay," Samoa Air Chief Executive Chris Langton told the Journal.
Langton said that while a heavier passenger flying on Samoa Air would pay more, the airline would ensure the bigger passenger has more room.
"We are like a shopkeeper; we are selling weight," he said. "But with the weight goes the responsibility of being able to seat the passenger comfortably."
Even though Samoa Air charges by the pound, many of the world's airlines have been reluctant to charge based on a passenger's weight because of discrimination concerns, the Journal said.
Some carriers in the U.S., including Southwest Airlines, do require passengers unable to fit into a regular coach seat to buy an extra ticket on full flights.
Samoa Air, which started up in June, flies regularly between Samoa and American Samoa, along with several domestic flights.