They have now been given the choice of losing a day's pay or forfeiting a day's leave.
The move comes after widespread media coverage and condemnation of the university's actions.
The gun threat came from an anonymous post on online bulletin board 4chan, which promised a shooting on Otago's campus on October 7.
At the time, police said they were taking the threat seriously.
Staff learnt by email at 5pm yesterday that ''issues have been raised regarding the treatment of leave'' for staff who did not come to work the day of the threat.
In the message, human resources director Kevin Seales defended the university's original decision, saying ''we felt that this was the fairest approach''.
''Taking annual leave was also, in our view, likely to be preferable to the default legal option, which is that the day would be unpaid,'' he said.
Staff were now free to choose not to be paid for that day, rather than forfeiting a day of annual leave.
''If you feel there are special circumstances justifying discretionary leave ... these will be considered by divisional heads,'' he continued.
''Sick leave is also available for stress-related or other illness.''
In a statement yesterday, Mr Seales said ''fewer than 1% of staff (numbering 48 in total) have booked annual leave for Wednesday, October 7''.
It is unclear if that comprises all staff members who did not attend work that day, or only those who complied with the university's order to record their absence as annual leave.
Mr Seales also said the university was ''incredibly grateful'' to the staff who did go to work, some taking on extra work to cover for absent colleagues.
Tertiary Education Union organiser Shaun Scott said the change ''does show a willingness to acknowledge they got it wrong''.
The union was not entirely satisfied with the university's amended decision, but Mr Scott was ''pleased that they've ... opened the opportunity to a further discussion''.
''We don't believe they've resolved the situation.''
The union had been considering legal action, and that was not off the table, Mr Scott said.
''We'll look at what it is that they're proposing and get a legal view on that,'' he said. The university's new approach remains at odds with at least one other institution that has dealt with a gun threat, the University of New South Wales.
When UNSW officials were made aware of an anonymous shooting threat to its campus earlier this month, also posted on 4chan, they issued a notice that ''those who would prefer to leave campus will not be penalised''.
Otago employment law expert Prof Paul Roth said last night the university's original approach of docking annual leave retrospectively had breached the 2003 Holidays Act. And its new approach might remain on shaky legal ground.
''They're making the rules retrospectively,'' he said.
''They should've let people know on the day. That principle still stands.''
Given the health and safety risk, employees should have been informed beforehand exactly what would happen if they did, or did not, go to work.
He also said there was an obvious logical gap in the university's reasoning, because it probably would not be taking this approach if the threat had turned out to be genuine.
''What if people had been shot? [Would] they still ... act this way?''Employment decisions had to be made on the basis of the information staff had on the day of the threat, he said.
Otago law professor Andrew Geddis, who went to work the day of the threat, said the university did not seem to be motivated by ''fairness'' for staff who worked that day.
''The claim from the university, that they're doing this out of a sense of fairness, doesn't seem to be driven by demands of the staff themselves,'' he said.
''Although I went to work and made a judgement that I probably would be safe, I certainly felt very different on that day than I did on others.
''I can accept that others would find that a reason to keep away.''
Prof Geddis said he had spoken to many colleagues who worked that day, and he had yet to hear any allegations of unfairness.
''No-one's expressed any unhappiness with the people who stayed away.''
