The airline introduced the policy in January, saying it would make flying safer.
Chief Executive, Chris Langton, told Radio Australia's Pacific Beat families have benefited the most.
"People who have been most pleasantly surprised are families, because we don't charge on the seat requirement even though a child is required to have a seat, we just weigh them," he said.
"So a family of maybe two adults and a couple of mid sized kids and younger children can travel at considerably less than what they were being charged before."
Samoa Air started flying within Samoa in 2012 and has expanded to now connect a number of Pacific island nations.
The "pay by weight" booking system requires passengers to type in their weight on the airline's online reservation system where their fare is calculated.
Rates range from $1 a kilogram on the airline's shortest domestic route to about $4.16 per kilogram for travel from Samoa to American Samoa.
The rate includes a customer's body weight and baggage.
Mr Langton says while it may take a while for customers to get used to the system, it also addresses safety concerns in the company's fleet of small aircraft.
"People have always travelled on the basis of their seat," he said.
"Aeroplanes don't run on seats, they run on weight.
"The smaller the aircraft you're in, the less variance you can accept in terms of the differences in weights between passengers."