Tenants paid an average of £549 per month in May, with rents rising across each region.
Your Move’s monthly buy-to-let index suggests the new land and buildings transaction tax (LBTT) has pushed up prices.
Glasgow and Clyde saw the steepest increase in rents, up 1.9 per cent from April to £549.
However, the region has also experienced the biggest decline in rent on an annual basis, with tenants paying 3.2 per cent or £17 less than the same month last year.
In Edinburgh and the Lothians, rents rose 1.7 per cent, or £11, from April to a record high of £662 per month.
The area has seen rents soar by 11.6 per cent, or £69, since May 2015, powered by the growing proportion of higher-paying jobs compared to the availability of homes.
Your Move Scotland lettings director Brian Moran said: “Rents are rising rapidly as a result of the new land and building transaction tax surcharge for buy-to-let properties.
“This tax hike has dissuaded landlords from investing in the sector, leading to a shortage of homes to rent, compared to the demand for housing.
“With the limited supply of rental properties, potential tenants have been forced to compete to secure homes, pushing up rents.
“The introduction of this anti-landlord legislation from Holyrood has ensured the cost of the policy has hit tenants hardest.”
According to the index, the proportion of late rent increased to 12.5 per cent of all rent due in May, compared to 11.6 per cent in April.
Tenant arrears have also deepened on an annual basis, with late rent standing at 8.8 per cent in May 2015.
Mr Moran said: “Tenant finances improved over the winter months, but it appears spring has been a tougher test.
“With employment in Scotland falling by 48,000 between February and April, some tenants may be struggling to make ends meet.
“However, on a positive note our research shows fewer tenants are falling into serious rent arrears, where they are more than two months behind in their rent.”