The alternative flag will fly on the Auckland Harbour Bridge ahead of a referendum to decide if it will replace the current New Zealand flag -- a move slammed as desperate by NZ First leader Winston Peters.
The black, white and blue silver fern design will fly on the bridge from Friday, and will fly alongside the current flag.
"Having the two flags flying side by side around New Zealand will help people compare the designs before making a decision in the final flag referendum, which runs from March 3 to March 24," Deputy Prime Minister Bill English said.
The decision has been criticised by Mr Peters, whose party is staunchly opposed to the flag change process.
"They have no statutory right to do it -- this is just a blatant attempt by the Prime Minister to put his fern flag on the same level as our national flag," Mr Peters said.
"Mr Key and National know they face humiliation in the referendum. This latest flag flying ploy shows they are desperate not to be losers.
"To fly the referendum flag winner beside the New Zealand flag is an exercise in deception and suggesting that it has the same status. Legally it has none."
Transport Minister Simon Bridges said he approved the request from the Flag Consideration Project to fly the alternative flag on the Auckland Harbour Bridge alongside the current flag from January 22 to March 24.
"The proposed alternative flag will be flown alongside the current flag each day on the Auckland Harbour Bridge until the end of the referendum period, except for Waitangi Day when the current flag will be flown alongside the Tino Rangatiratanga flag."
Presently, only three flags, alongside the New Zealand flag, are allowed to fly on the Auckland Harbour Bridge -- the Tino Rangatiratanga flag on Waitangi Day, the Australian flag on Anzac Day, and the Merchant Navy flag on Merchant Navy Day.
Earlier this month, a Weekend Herald editorial called for the alternative flag to be flown from the Auckland Harbour Bridge, arguing that the "most visible poles in the country" should be utilised to give people an idea of how the flag looks in real life.
The silver fern flag with black, white and blue colours will go head-to-head with the existing flag in a second referendum in March, which will decide whether New Zealand changes its flag for the first time in more than 100 years.
Whether New Zealanders choose to ditch or keep the current flag, March 24 will bring to a close a process that officially began in October last year when Prime Minister John Key announced that a two-stage referendum would be held on the issue.