"This is the fairest way of travelling," chief executive of Samoa Air, Chris Langton said.
"There are no extra fees in terms of excess baggage or anything - it is just a kilo is a kilo is a kilo," he told ABC Radio.
Like many Pacific island nations, Samoa has a serious obesity problem and is often included in the top 10 countries for obesity levels.
"When you get into the Pacific, standard weight is substantially higher (than south-east Asia)," he said.
"That's a health issue in some areas. (This payment system) has raised the awareness of weight," he added.
Under the new system, Samoa Air passengers must type in their weight and the weight of their baggage into the online booking section of the airline's website.
The rates vary depending on the distance flown: from USD 1 per kilogramme on the airline's shortest domestic route to about USD 4.16 per kilogramme for travel between Samoa and American Samoa.
Samoa Air operates BN2A Islander and Cessna 172 aircraft.
Langton said he believed it to be a system of the future, and added that "the standard width and pitch of seats are changing as people are getting a bit bigger, wider and taller than they were 40 to 50 years ago".
He also pointed out that families travelling with small children could end up paying far less with the pay-by-weight scheme.
"A family of maybe two adults and a couple of mid-sized kids ... Can travel at considerably less than what they were being charged before," he said.
Some airlines in the US already force obese passengers who cannot fit in a single seat to pay for two seats, but this is the first time a per-kilo rate has been used by an airline.
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