Mr Mulholland said he attended all six hui around the country.
One hui at Te Tii Marae told the panel it did not want the 1834 independence flag included in the ballot.
"That is why that was not one of the flags that was short-listed."
The panel also met relatives of Te Kawariki founders, the northern protest group that had been involved in the design of the tino rangatiratanga flag, and they did not want that flag to be involved in the process.
"Looking back, I don't know how we could have done things differently to better engage with Maori."
He did not know why turnout was low in the Maori electorates or why the silver fern was rejected.
He said the link between Maori and the silver fern was historically strong, from the Maori All Black captain Tom Ellison suggesting it for the All Black uniform to Maori proverbs about it.
Labour leader Andrew Little said the preference for the status quo could be partly due to the significance of the Maori relationship with the Crown.
"Going back several decades, the House of Lords has typically shown a much greater sensitivity to indigenous land rights than our own courts here, until recently."
And early efforts by Maori to get redress for Treaty breaches were done in trips to Britain.