Even under the original lockdown which began in March, banks had kept some branches open under limited hours in order to provide services to customers who do not have access to internet banking or are unable to use ATM machines.
New Zealand Bankers' Association Roger Beaumont said in a statement that the Ministry of Health's order for August "did not technically allow banks to open branches to serve customers".
Bloomfield's outright rejection of the Reserve Bank's application prompted the industry to immediately close branches.
"We were advised this morning by the Ministry of Health that banks do not have an exemption to operate under alert level 3 and have to immediately close the nine branches we had open in Auckland," BNZ said in social media posts on Monday.
By Monday afternoon, Bloomfield's concerns were seemingly satisfied, approving the Reserve Bank's original application.
While the reasons for the change of heart remain unclear, the Prime Minister's office confirmed that it had become involved on Monday.
"We were made aware by banks that they had closed their Auckland branches due to not being granted an exemption from the Ministry of Health to trade under level 3," a spokeswoman for the Prime Minister said.
"We need New Zealanders to be able to access money and bank services and we are aware that for many people this is done via a bank branch. So officials discussed the matter and the director general of health signed an exemption yesterday afternoon."
Why banks were not included in the original order was unclear last night.
MBIE, the Reserve Bank and the Ministry of Health variously referred questions to each other about the issue on Tuesday.
A spokeswoman for the Ministry of Health said the original application "did not meet the criteria for an exemption".
The ministry then received "further information" allowing it to be approved, but she would not say what, citing "privacy reasons".
Additional reporting Tamsyn Parker