The subway outlet was closed on Wednesday because it did not have the correct Dunedin City Council paperwork in place. It reopened the following day.
Council chief building control officer Neil McLeod said yesterday retail premises needed either a code compliance certificate or a certificate for public use to be able to accept customers on to their premises.
The new Subway store had neither and was asked to close until it did.
Certificates for public use are issued when stores comply with safety regulations such as fire exits.
Subway's certificate had only been applied for on Monday, he said.
Under the Building Act, councils were allowed up to 20 working days to complete such applications, but his staff had "expedited Subway's application quickly" so it could reopen as soon as possible.
A code compliance certificate could only be approved when all building work on a new retail outlet had been completed, Mr McLeod said, but a certificate for public use could be applied for at any time.
He said he accepted the hitch with the Subway store was an administrative error at Subway's end, but said last-minute applications were lodged once or twice a month and were frustrating for council staff.
"People, invariably retail outlets, leave applications to the last minute all the time . . . Then they expect us to react quickly because their application is urgent.
"We do what we can, but we don't have five guys sitting around twiddling their thumbs waiting for work. We would urge people to plan ahead and apply early."
Mosgiel Subway franchisee Julian Field could not be reached for comment yesterday.