The charity said this was disproportionate to the sector's size, which is 13% of housing in Scotland.
Homeless applications have decreased by a third in the past five years but the Shelter said the statistics did not tell the full story.
It said it was important that vulnerable households were supported before they were pushed into crisis.
According to the latest Scottish government figures, the proportion of  homeless applications that come from the private rental tenants rose from 13% 2008-09 to 18% in 2013-14.
However overall homelessness in Scotland fell by 34% during the same period, official statistics showed.
Graeme Brown, director of Shelter Scotland, said: "Whilst the headline figures show that homelessness applications are down by one third in the last five years, which is welcome, our analysis shows it is not all good news for homeless people in Scotland.
"The 36,457 households making homeless applications, a youth homelessness rate at 13.7 per 1,000 and a rising proportion of homeless applications from the private rented sector signal that, although there are movements in the right direction, there is still a long way to go."
"With the significant weakening of the welfare state in recent years, it is more important than ever to ensure that vulnerable households are offered support before they are pushed into crisis."
The report, 'Homelessness in Scotland 2014: Getting Behind the Statistics', has been released ahead of Shelter Scotland's annual conference later this month.
Housing minister Margaret Burgess said: "Homelessness in Scotland is falling and the number of homeless applications from the private rented sector has actually fallen by 21% since 2008/09.
"The Scottish government is working closely with local authorities and their partners, and with Shelter, to prevent homelessness, increase the number of affordable homes and address the issue of empty homes. Where people do become homeless, our focus is on finding the best outcomes."
Almost a fifth of homeless applications now come from the private rented sector, according to Shelter Scotland.