Les Bore, an Ahipara surf school operator who was one of the first people on the scene, thought the whales had been attacked by orca.
They were covered in bite marks and were bleeding, with bloody eyes, Mr Bore said.
"Me and my friend tried to refloat them, successfully getting them back into the water but they couldn't swim properly," he said. "We tried for two hours but realised they must have internal damage."
But whale expert Jo "Floppy" Halliday, from Whale Rescue, did not believe the bite marks were caused by orca.
The marks were commonly caused by other pygmy whales as they tend to "nibble each other like rough play" while playing or mating, she said.
"They are a deep water ocean-going whale; they are more likely a bite mark from another [pygmy whale] or a lover — most of them are promiscuous."
Ms Halliday was at a loss as to why they stranded but she said it was extremely unusual to find them in New Zealand waters. The whales were found in Australia and towards the tropics, she said.
The whales were thought to be part of the same pod and it was possible one had got into trouble or got sick and the others followed it inshore.
The king high tide, which also caused chaos with the rescue, could have caused confusion with the whales' sonar, she said.
The whales were not emaciated so had not been starving, Ms Halliday said.
The physical distance between the whales and Monday's rough sea conditions — with 1.5 metre swells and onshore winds — made refloating difficult, she said.
The whales also needed time to adjust their balance, after being left on their sides overnight Sunday. Ms Halliday was hoping to move the whales late yesterday, then refloat them today.
"It's a little bit concerning being so far away from each other. By regrouping, it means that the people are safe as well as the whales."
Awanui local Aaron Kem had formed a bond with one of the whales — an adult female nicknamed "Lucy Liu", who was stranded near Maunganui Bluff.
Mr Kem was at the scene at 8am yesterday and helped calm the whale, which was initially thrashing its tail and "making barking noises".
"They said it's formed a bond with me. I've been here with her the longest so I'm going to stay with her," Mr Kem said.
Seeing the small whales alive was "great", he said.
Meanwhile, the sperm whale which died near Dick Urlich Drive on Tokerau Beach, Karikari Peninsula, had been seen swimming around Doubtless Bay for the last week.
It was not known what caused its death nor if the whale strandings were connected.
But Tokerau Beach local Robert Urlich was convinced the death was caused by mircoplastics which are found in the ocean.
"It's not just the whales but the whole of the marine life, and not only the marine life but the birds that feed on the small fishes, they've been affected too," Mr Urlich said.
"It gets us too in the longer term — humans — and it's humans that have caused it in the first place."
The 15m, 30-tonne whale was pulled as high as possible from the water on Saturday. Samples were taken before the whale was flensed.
DoC community ranger Jamie Werner said DoC staff had stayed with the whale 24/7 since Friday afternoon.
