Three of the five alternative flags feature silver ferns.
Mr Mulholland said the All Blacks' influence on the vote could "go either way". The existing flag was displayed behind the team when they sang the anthem on Sunday, and could be more closely associated with the victory.
Mr Mulholland said Prince Charles' visit this week would be, at the least, a reminder of New Zealand's ties to "Mother Britain" and the Union Jack.
However, he also said that just three out of 53 Commonwealth countries outside the UK - New Zealand, Tuvalu and Australia - still carried the Union Jack on their flags.
Monarchy New Zealand spokesman Sean Palmer said countries such as Canada had changed their flags decades ago but had given no thought to distancing themselves from the Queen of England.
"The connection between the monarchy, New Zealand and its flag is really not affected by its design," he said.
Returned and Services Association national president BJ Clark, whose organisation wants to retain the existing flag, said he observed a large number of fans flying it at the Rugby World Cup final.
"I was personally surprised ... to see so many," he said.
"I think it's an indication that the majority of New Zealanders are still for the retention of the current flag."
Labour Party internal affairs spokesman Trevor Mallard said he believed the events would make little difference to the vote, especially because the existing flag was not an option in the first referendum.
He said none of the alternative flags bore a close resemblance to the silver fern on the All Black jersey. The most similar, the black and white fern design, had proven unpopular in public polls, he said.