Occupancy at some Wellington government departments has been down by as much as 70 per cent during level 2, despite repeated calls for public servants to return.
All regions south of Auckland moved to alert level 2 at 11.59pm on Tuesday last week.
Official government advice states you can go to work at level 2, but all workers should keep at least 1 metre apart in offices, where possible.
There is no limit on the number of people that can be in a workplace, as long as everyone can safely physically distance.
Prime Minister Jacinda Ardern and her deputy Grant Robertson have been questioned about whether public servants should be heading back to work, with Wellington still resembling a ghost town despite the shift down alert levels.
At Friday's Covid briefing, Robertson said he was "confident" public servants would return to the capital's CBD this week.
"I certainly want them to as MP for Wellington central."
Ardern on Tuesday also said they were "encouraging" people to come back into the city.
"We've got all the measures required to keep people safe while they're out and about so they should feel free to come back into the city, frequent their favourite local cafe, pop in to their local retailer and definitely support local."
But despite this encouragement from the top, a number of government departments aren't fully open yet even if staff wanted to return, citing level 2 restrictions and the need to physically distance.
Waka Kotahi, the NZ Transport Agency, can seat 1001 people in its Wellington office. Staff were allowed to return on Friday, three days after the move to level 2 - but on Friday only 96 people turned up - just 10 per cent of available capacity.
A spokesperson said that increased to 332 people, or 33 per cent capacity, on Monday.
"We expect to see more people in the office over the coming days and weeks."
ACC wouldn't provide a number, but said the "majority" of its Wellington-based employees are continuing to work from home rather than return to the office.
"As our Wellington office is a multi-storey building with a significant number of people usually based there, under Covid level 2 protocols, physical distancing is unlikely to be possible in meeting rooms, kitchens, lifts, stairwells and bathrooms.
"At our other offices around the country, outside Auckland, the majority of our people are working in the office.
"This is because these buildings are largely single level with a lot of space, enabling people to easily maintain physical distance for the majority of the time and wear face coverings in common areas like kitchens and bathrooms."
The Ministry of Business, Innovation and Employment, one of the largest public departments, has approximately 3200 people across 11 sites in Wellington. It has reduced capacity to about 50 per cent to allow for safe physical distancing at level 2.
Deputy Secretary Richard Griffiths said their sites were at around 35 per cent occupancy on Monday. They too were anticipating an increase in the coming days.
New Zealand Trade and Enterprise was in the same boat, reporting just under 30 per cent occupancy this week, out of a workforce of 140 people.
Just 10 per cent of staff at Worksafe have returned to the office in Wellington after reopening in level 2, however occupancy was only at 40 per cent pre-lockdown.
The Ministry of Health, with 1260 employees in Wellington, would not say what occupancy was, but said the return of staff was being '"staggered".
The Ministry of Education was also unable to provide numbers, saying they "change daily". Nor could the Ministry of Environment or the Ministry of Social Development.
The Ministry for Primary Industries can safely accommodate all its staff but was unable to estimate the percentage that had returned because numbers changed daily.
The Ministry of Transport is only allowing 50 per cent occupancy during level 2, to allow enough room for physical distancing in shared spaces such as the kitchen and bathrooms. It said numbers had gradually increased with around 95 out of 200 staff in the office.
At the Department of Conservation, 250 people out of 585 were in the building on Monday.