Adventure tour company Intrepid rescued the Australians by helicopter on Thursday local time (Friday AEDT) after weather conditions improved.
Company spokeswoman Meg Koffel said 17 of the 29 Intrepid travellers stranded at the site since Sunday had now been airlifted from the town of Aguas Calientes to Ollantaytambo, at the start of the Inca trail.
From there they were taken by bus to Cusco, about two hours away.
Four other Australians aged over 50 were given priority and choppered out of the stricken area on Thursday.
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Another seven Australians remain among the final group of 12 Intrepid travellers at Machu Picchu and it is hoped they will be rescued in coming days.
"The good news is we've been able to get over half the group out," Ms Koffel told AAP.
"We will know more in the next few hours, but we're hopeful that we will be able to get more of them out in the next few days, depending on the weather.
"The 17 passengers we have been able to get out to date are all in good spirits, they are tired but they are healthy and I understand they're contacting their families to let them know they are in Cusco and safe."
Heavy rain and mudslides had stranded up to 2,500 travellers visiting the ancient ruins, high in the Andes Mountains.
Ms Koffel said some passengers were keen to continue their tour despite their ordeal, but Intrepid would help those who wanted to head home with their insurance.
Australians unable to leave the affected area are advised to call DFAT's consular emergency centre on +61 2 62613305.
DFAT has established a hotline for concerned friends and relatives of travellers, on 1300 555 135.
