The survey of 1000 SME operators included 12 per cent in the tourism sector. The survey covers business owners and operators from sole traders to mid-sized businesses of 20 to 199 staff.
A Herald series this week has highlighted the financial spinoff from the tourism boom but also found the pressure to find workers and this is reflected in the survey.
The survey finds this is particularly the case in Queenstown and Auckland.
Rising house prices have made it harder for 28 per cent of tourism operators to recruit and retain staff, nearly twice the SME average.
MYOB general manager Carolyn Luey said this could put the brakes on growth.
"Many businesses may well be held back by how expensive it is becoming for staff to find accommodation - especially in key visitor markets like Queenstown and Auckland," she said.
Many workers in the sector can expect pay rises with a quarter of all tourism SMEs intending to increase the amount they pay their staff this year and nearly a fifth will be offering more fulltime roles.
Luey said 37 per cent of businesses expected increased competition and others were reporting growing pressure from increases in the cost of fuel, narrowing margins and the burden of compliance.
"What we are seeing here is a market that is doing very well, but needs to keep a close watch on the fundamentals in order to prevent costs and pressures from blowing out and affecting the bottom line."
She said there were also some fundamentals New Zealand needed to address as a country such as affordable accommodation for staff, labour shortages during seasonal peaks and the cost of compliance especially around health and safety and resource management.
"New Zealand has a fantastic industry in tourism, but we need to take a very careful look at how we are managing its growth and planning for the future."