Maori Party MP Hone Harawira says he is appalled that Transit allowed the European Union flag to fly on Auckland Harbour bridge.
"I'm referring this to the Race Relations Office," said Mr Harawira.
"It's an insult to Maori, and an insult to the intelligence of all New Zealanders.
"Transit can't say that we won't fly your [Maori] flag because it doesn't represent a country, and then go and fly another one that doesn't represent a country.
"It's hypocritical. Heads must roll."
The flag flew yesterday, in recognition of Europe Day.
The observance was requested by the European Commission delegation to New Zealand.
Generally, Transit considers requests from nations wanting to commemorate their country's national day, but Transit regional manager Peter Spies said yesterday that the criteria also included flags recognised by the New Zealand Government.
As the European Union flag had in the past flown from government buildings, the policy was being adhered to.
In February, Maori sovereignty group Ata Tino Toa sought permission from Transit to fly the red, black and white tino rangatiratanga flag from the bridge to commemorate Waitangi Day.
Their request was denied, and Mr Spies said there had been no change in policy that would allow the tino rangatiratanga flag on the bridge in future.