Port of Tauranga chief Mark Cairns said the port managed to get three ships through the entrance in the early hours of Saturday morning before the protest began.
But Mr Cairns said it was disappointing the protest delayed a salt vessel.
"It was a two-to-three hour delay which is more of an inconvenience," he said. "If it was delayed longer than that it will be an issue."
He urged the iwi leave the port out of any issues and instead engage with the Crown or Hauraki.
"They have communicated they do not have any beef with the port. I just find it very frustrating."
Mr Cairns reiterated he respected the iwi's right to a peaceful protest but said it was frustrating.
"I am really annoyed," he said. "We have what I considered to be a strong relationship with Ngai Te Rangi ... it is really not safe what they are doing."
Harbourmaster Peter Buell said there were about a dozen boats taking part in the protest on Saturday, as well as a waka.
"It was a well organised, peaceful demonstration and it was great to see them taking safety so seriously."
A police spokesperson said police worked with the Harbourmaster to ensure everyone's safety. "There were no issues."
Bureta resident Arthur LeComte was there to support the protest.
He said the protest was not aimed at the Government or the port.
"But this is how the people get recognised and that is what it is about."
Mr LeComte believed it was the right thing to do.
"Safety is not compromised. Everyone is going to follow health and safety guidelines."
As part of the protest, about 200 supporters performed a flash haka on the side of Mauao (Mount Maunganui) to coincide with the water protest.
Lead co-ordinator on Mauao Meremaiha Aloua said everyone was there to stamp their ground in terms of their moana and claim back what was theirs.
She said the message was directed at the Crown and Hauraki.
Charlie Rahiri, of Ngati Ranginui, said he was there to support Ngai te Rangi.
"We are sending a signal to the Crown that they cannot keep doing these secret deals."
He said there were hapu from Katikati, Te Puna, Wairoa, Matakana and Matapihi on the side of Mauao to perform the haka.
"We are standing together. We have our internal battles but we will defend our Moana together."
Ngai Te Rangi chief executive Paora Stanley said the protest was a humbling experience "to watch our people express themselves in a way that asserts mana".
Calls to the Hauraki Collective have gone unanswered.
On Thursday, a spokesperson for Minister for Treaty of Waitangi Negotiations Chris Finlayson said there had been no secret deal. The Waitangi Tribunal confirmed in 2004 that iwi of Hauraki had customary interests in Tauranga Moana, particularly in the Te Puna and Katikati area, the spokesperson said.
"The Minister also understands there are rumours of a deed signing for Pare Hauraki. No date has been set for any such signing. Officials informed Tauranga iwi of that fact last week."
