Samoa Airways flight OL731 arrived before 11am on Tuesday, carrying dignitaries and passengers including Samoa's Prime Minister Tuilaepa Sa'ilele Malielegaoi.
The airline has been rebranded from the state-owned Polynesian Airlines.
The new airline came about after the Samoan Government announced in May that it was walking away from Virgin Samoa, its joint venture with Virgin Australia Holdings, to go it alone, RNZ reported.
Virgin Australia had announced plans to start flights from Auckland to Apia, but since then the Samoan Government had denied it permission to operate the route.
The airline, however, is allowed to operate services from Brisbane and Sydney to Faleolo International Airport.
It's an ambitious timetable for Samoa Airways.
The airline's sole Boeing 737-800, leased from Iceland Air, will operate six return flights from Apia to Auckland a week and twice-weekly services from Sydney to Apia.
Speaking at a welcome event at Auckland Airport, Minister for Samoa Airways Lautafi Fio Selafi Purcell said he hoped the airline would grow to challenge Air New Zealand on the route.
"This is another opportunity for our people to allow our business to grow," he said.
The flights would also allow more mobility between the two island nations.
"Auckland is a second Samoa - and more and more Samoans are living in Auckland as their second home or their first home."
The airline's chairman Fe'esago Siaosi Fepulea'i said it was a good venture to be involved with.
"We've waited a long time for this, our airline [has been] controlled from overseas, we are now back where we should have been in the beginning," he told the gathering.
Fepulea'i said he welcomed "criticism for the betterment of our services", but he challenged those "knocking" the airline and for Samoan people to back its airline.
"It [the arline] belongs to Samoa," he said.
Auckland Airport chief executive Adrian Littlewood said Samoa Airways was the 31st international airline to operate at the airport.
"Connecting Samoa and Auckland, in particular, means a lot for our neighbours in the community and staff," he said.
Also at the welcoming ceremony were Samoan dignitaries, Associate Minister for Pacific Peoples Carmel Sepuloni and Auckland Mayor Phil Goff.
Sepuloni said the flights would lift trade and tourism between the two countries and bring closer ties.
The associate minister said the service would tie in well with upgrades to Faleolo International Airport in Apia.