A Legislative Assembly committee is examining the territory's rates system as it relates to commercial property owners, in the wake of re-valuations that caused commercial rates to soar in some parts of the city.

Property owners in areas including Braddon, Phillip and Fyshwick, like most unit owners affected by recent changes to unit valuation calculations, have faced big increases to their rates bill due to the re-valuations.

It follows an earlier inquiry into changes to rates calculations affecting thousands of Canberra unit owners, the recommendations of which the ACT government has largely ignored, other than to agree to a public review of its tax reform program.

During Wednesday's hearing, Civium chief executive Doug O'Mara told the committee he was concerned recent re-valuations of properties were not only affecting property owners, who often had no choice but to pass on the costs, but also small businesses leasing such premises.

He said the commercial property market was facing a perfect storm of economic headwinds including high vacancy rates, banks tightening their lending criteria and rising rates bills, which he described as "the biggest issue" facing the sector.

Despite new Property Council figures suggesting average office vacancy rates had fallen from about 12 per cent to 11 per cent in the last half of 2018, Mr O'Mara said in the second-tier market, the vacancy rate was likely closer to 16 per cent.

He said the second-tier market was being challenged by newer office buildings offering more attractive tenancies, and some owners were not bothering to rent properties out at lower returns, which could affect property values and, in turn, their finance.

The committee also heard about the effects of recent re-valuations of suburbs being redeveloped from industrial to mixed use precincts, which caught some property owners and tenants off guard with unexpected rate rises.

Some owners saw rates rises in the order of $100,000, with the increases most keenly felt in Phillip, where the total value of the 108 properties affected rising 79 per cent from $100 million to $179 million in 2017, or about $730,000 on average per property.

ACT committee chairman of the Australia Property Institute, Greg Cummins, said the problem was partly due to the value of blocks in such areas not being re-assessed regularly, and when re-valued, they rose 10 to 20 per cent in one year.

Mr Cummins said he was also concerned the territory government valuers were a small team based in Treasury's revenue office, and that they could face conflicts of interest in providing valuations, particularly in appeals.

In most other jurisdictions, official state government valuers sit in an Office of the Valuer-General, an independent statutory authority tasked with valuing properties without government interference, given the key role property values play in determining revenue.

Mr Cummins said the issue could arise when owners tried to appeal valuation increases to the revenue office, suggesting the valuation office did not necessarily have the same level of independence as similar offices in other jurisdictions.

He also said some larger institutional investors were wary of the high costs of investing in commercial property in the ACT, and others had sold their land because of it.

But Mr Cummins said the costs of businesses moving interstate for those already in Canberra meant that often they would 'grin and bear it'.

An ACT Treasury spokeswoman said the five valuers in the valuation office were full or provisional members of the institute and had to meet professional development requirements to stay certified, as well as meet the public service code of conduct.

"Five members of the [seven] valuation staff are fellow, associate or provisional members ... and most have tertiary qualifications to postgraduate level," she said.

"Current arrangements for the valuation branch represent a balance between administrative efficiency, effective cost management and appropriate qualification and skills to deliver best practice outcomes."

Clarification: This article previously stated Mr Cummins was ACT branch president of the API. He is ACT committee chairman.