The report found that Perth's average nightly rate for a hotel room escalated by 19.5 percent over the 12 months to December 2008.
While Darwin experienced the strongest demand in accommodation, up by 9.3 percent.
Michael Thomson, National Director of Hotels and Leisure at Colliers International, said that the two cities strong performances resulted primarily from the resources sector.
"Both cities comprise some of the most productive resource regions in the country, and the result in demand from this sector has supported the accommodation markets," he said.
"Darwin in particular holds a cross section of key drivers including being a regional government and defence location, a tourist destination and strong infrastructure investment."
While Australia's tourist accommodation market will perform slower for the remainder of 2009, the nation's major hotel markets are positioned to make a quick recovery with limited supply on the horizon, according to the report.
The further deterioration in Australia's economy which has lead to a technical recession, has weakened the country's hotel sector.
"The combination of reduced corporate and leisure activity and spending has resulted in a decline in occupancy levels, which has put downward pressure on Revenue Per Available Room (RevPAR) rates," said Mr Thomson.
"However, for cities such as Sydney, Brisbane and the Gold Coast, limited hotel supply on the horizon will greatly benefit existing hotel operators when demand improves."
The report found that occupancy levels are down from the highs achieved in 2007. And performance is varied between capital cities.
It was a modest start to 2009 with three major hotel transactions including the Hyatt Adelaide ($75 million), Darwin Airport Resort ($21 million) and Cradle Mountain Lodge in Tasmania. There is a significant amount of hotel assets currently for sale in Australia, representing a potentially high level of activity for the year.
"The weight of demand is primarily from investors in neighbouring Asian counties who are looking for value assets. However, there is still a gap between vendor and purchaser expectations," said Mr Thomson.
Sydney
Average room rates in Sydney's hotel market decreased moderately by 3 percent to $184.69 and it experienced a slight decrease in room nights sold for the 12 months to December 2008, compared to the prior 12 months.
Colliers International predicts that once the economy recovers, Sydney's hotel performance will be one of the quickest to recover. This is because there is limited hotel supply on the horizon and any improvement in demand should result in immediate RevPAR gains for hoteliers.
Melbourne
Room nights sold in the 12 months to December 2008 remained the same in Melbourne compared to the previous year, as its events calendar is expected to maintain the city's strong demand for accommodation in the medium to long-term.
"Melbourne's accommodation market will also benefit substantially from the investment in tourism infrastructure and volume of new quality hotel accommodation available for visitors," said Mr Thomson.
Occupancy in Melbourne decreased but only marginally, down by 0.7 percentage points to 80.4 percent. Average room rates experienced solid improvement, up by 6.1 percent to $171.20.
Brisbane
The Brisbane hotel market experienced the second-highest demand for accommodation in Australia over the 12 month period, at a 5.7 percent increase in room nights sold. However, occupancy was down 2.4 percentage points to 78 percent.
"Brisbane is underpinned by a strong resources sector," said Mr Thomson.
"While hotel trading conditions in Brisbane CBD will be slower this year, the city is well placed to bounce back quickly when the economy improves. In addition, there is limited new hotel development in the pipeline and existing hotels will see the benefits of increased demand."
Cairns
The tourism industry in Cairns has been through a poor performing year for accommodation providers characterised by falling hotel occupancy rates of 5.7 percentage points to 61.9 percent, and the lowest recorded RevPAR, which fell by 9.3 percent to $74.13.
"It is expected that by combining effective marketing, new attractions and increased air capacity, the Tropical North tourism industry will see a return to better trading conditions," said Mr Thomson.
Perth
Perth's average nightly rate for a hotel room was $159.36, which grew by 19.5 percent. The city also experienced an increase in demand by 5.6 percent.
The strongest improvement in average room rates was also recorded for Perth, which rose by 19.5 percent to $159.36.
"In terms of hotel room rates, Perth has gone a long way in closing the gap with the Eastern Seaboard," said Mr Thomson.
Darwin
Darwin was the standout city in the report, which experienced the strongest demand in accommodation, up by 9.3 percent, as mentioned above.
It also recorded the highest occupancy improvement, with a rise of 1.1 percentage points to 74.9 percent, and strong RevPAR growth of 12.7 percent, increasing to $105.01.
"Investment in tourism infrastructure such as the Darwin Airport upgrade and the Darwin Waterfront, which includes the new Convention Centre, will pave the way for demand growth in the future and improve Darwin's tourism profile," said Mr Thomson.
