The increase facing apartment owners stems from a change to the way unit rates are calculated that took effect in July.

That change has increased the average annual rates bill for unit owners by $250 this financial year, with a further average $115 rise expected from July next year.

A one-off $100 rates rebate has insulated ratepayers from the full effects of the $250 average increase this year.

The rates hike means an "average" unit owner who paid $1156 in rates in 2015-16, will pay on average an extra $365 - or 31 per cent - on their annual rates bill from July next year, before the additional two years of seven per cent rises are added to their bills.

But Owners Corporation Network president Gary Petherbridge said he had already seen many rates bills for this year that had an increases of as much as 100 per cent compared to the 2016-17 year.

Mr Petherbridge said the government's use of 'average' figures for units and houses created a 'false impression' and the new calculation method did not take into account the fact units took up less land than freestanding homes.

The change in the way ACT Treasury calculates rates for multi-unit dwellings is being phased in over two years from this July, as part of the government's long-term tax reform agenda.

ACT Treasury is now calculating unit rates based on the land value, then dividing that total by the number of units, replacing the previous formula that divided the land value by number of units, then calculated individual rates.

A Treasury spokeswoman said the changes aim to ensure unit owners, who hold 29 per cent of all rateable properties in the ACT, are paying a more proportional share of the territory's rates revenue, compared with owners of freestanding homes.

"The intention of the change is to ensure that rates on units are better aligned with those on freestanding homes," she said.

"Under the previous approach, there were instances of rates being lower for million-dollar apartments in Kingston than they were for average-priced houses in Tuggeranong, and this was not fair."

But Mr Petherbridge said that comparing a $1 million Kingston foreshore apartment to freestanding homes in Tuggeranong was not representative of the true situation.

"The more accurate representation of the situation is that there are many low cost one and two bedroom apartments versus big houses in Tuggeranong," he said.

Despite the change in rates for unit owners, some 32,783 units - or 72 per cent of all apartments in Canberra - remain in the lowest marginal rating category, below the $150,000 threshold.

Government figures show a further 11,032 units fall into the $150,001 to $300,000 bracket; 1433 fall into the $300,001 to $450,000 bracket; 485 are in the $450,001 to $600,000 bracket and 533 units are in the top, $600,001 and above ratings category.

The Treasury spokeswoman said in 2016-17, unit owners paid about 17 per cent of the government's total residential general rate revenue, a figure that would rise to 20 per cent this financial year.

"Units make up 29 per cent of all rateable properties in the ACT, demonstrating they are still not paying a fully proportional share of all rates revenue," she said.

But Mr Petherbridge said the real situation facing unit owners were rising rates, energy costs and body corporate levies, as well as "as developers refusing to contribute to rectify building defects".

"These strata buyers need government support, not financial punishment," he said.