"But we will not lose sight of the real cost, of those who died here on the site."
She said about 20 Māori and 12 British had died in the battle - and acknowledged Ngati Hine for embracing the memories of the 12 British.
She said the wider story of the New Zealand wars had often been under-acknowledged while wars overseas had been studied - which needed to change at schools.
"Let us teach it, let us learn it so students are aware how our country and our identity have been shaped by events like this."
Clarke said it was right to come together to mourn all those who died in the battle, whatever side they were on.
"I would like to extend my deepest gratitude for the respect and commemoration that has been afforded these 12 British men, and recognise the [Ruapekapeka] Trust's generosity and determination to find them."
She also read a message from British Defence Secretary, Ben Wallace, expressing gratitude to the people of Ruapekapeka for the respect they had shown to the British troops, and saying he was humbled by it.
Trust chairman Pita Tipene, said he had heard the stories from his mother – including about the alliance of Kawiti and Hongi Heke to prevent the Crown stamping on their mana and taking lands.
"In 2021 and beyond, not a lot has really changed. Māori are still to see fulfilment of the promise that was and is the Treaty of Waitangi."
Tipene said he was delighted that the Government was to ensure New Zealand history would be part of the school curriculum by next year.
He also had a word for those who believed monuments to "oppressors" should be destroyed.
"Our ancestors fought the British to the death, but nonetheless respected them as enemies."
Dame Patsy Reddy said Ruapekapeka bore the scars of a dark and troubled period in New Zealand.
"It was the first significant engagement of perhaps the most infamous of my predecessors, Sir George Grey."
She said Aotearoa now bore the responsibility of looking after the 12 men in the grave, and also acknowledged the hurt it had caused to Ngāpuhi - a hurt that was still to heal.
Last month was the 175th anniversary of the battle at the pā built by Ngāpuhi chief Kawiti, the pā's name translates as the "bats' nest" and it was known for its complex fortifications.
Sir George Grey had instigated the invasion of the pā - about 1300 British soldiers invaded it, 300 Māori fought alongside them. In the pā, Kawiti and Hone Heke led warriors outnumbered by the invaders by about four to one.
After weeks of firing and one day of bombardment, the British found the pā abandoned.
The Prime Minister's attention will turn to Waitangi tomorrow when she heads to Te Whare Runanga on the Treaty grounds to deliver her fourth speech as Prime Minister at Waitangi.
In her first address in 2018, Ardern told them she would return to be held to account for her actions for Māori as Prime Minister. She returns with a strong mandate: a strong majority for Labour.
The leadup to Waitangi has been marked by a rollout of announcements for Māori, including removing the ability for councils' decisions to establish Māori wards to be overturned by a referendum. The Government has also announced a $170 million investment fund for Ngāpuhi, pending the iwi's settlement for which talks have stalled.
Treaty Negotiations Minister Andrew Little and the Crown's chief negotiator for Ngāpuhi Sir Brian Roche are also in Northland.
Last year Ardern announced a new public holiday to mark Matariki and the Government is also moving to include more New Zealand history in the school curriculum.
