Samoa's Ministry of Health issued a directive on Saturday (local time) saying there was an increased risk of COVID-19 entering the country after New Zealand diagnosed its first case.
Ardern says it is up to each country what safety precautions they impose and how they deal with the disease.
"Ultimately, our Pacific Island nations are going to make their own decisions around how they wish to manage potential human-to-human transmission," she says.
She says she contacted Samoa Prime Minister Tuilaepa Sa'ilele Malielegaoi to give an update on New Zealand's measures and restrictions, but has no hard feelings towards the country's new flight restraints.
"Everyone has to make decisions based on their own health systems, based on their own requirements at the border."
The Samoan Ministry of Health is now also requiring all passengers who enter the country to have undergone a medical examination within three days before arriving in Samoa. The medical clearance report is required for check-in prior to boarding passes being issued.
"Due to New Zealand's close proximity to Samoa... the increased risk of COVID-19 entering Samoa has elevated from high to very high and its impact on Samoa's population remains catastrophic," a statement from Samoa's Ministry of Health says.
The frequency of flights arriving into the country will therefore be reduced to help prevent the disease entering Samoa.
Air New Zealand can now only send three flights per week from Auckland to Apia, half of what is normally scheduled.
Flights NZ958/959 on March 2, March 6 and March 8 are cancelled. Flights still scheduled to depart are NZ254/255 on March 3, March 5 and March 7.
Air New Zealand said in a statement it is working through schedule adjustments for the week beginning March 9.
"While these restrictions are expected to be disruptive to some customers planning to travel to Samoa, Air New Zealand understands the request, and will do what is necessary to comply with the requirements of the Samoan Government."
Customers affected by these changes will be directly contacted by Air New Zealand. People who booked through a travel agent will be contacted by their booking agent, the statement says.