The only sector recording an increase in activity was construction, whereas retail reported the sharpest decline.
Chief economist for Ulster Bank, Sebastian Burnside, said the survey was “good news” for the local labour market in June as companies started hiring again.
Northern Ireland was the only area of the UK where employment rose.
“Other aspects paint a more subdued picture, however,” Mr Burnside said.
“The expansion in output we saw last month was not sustained into June as new order inflows remained muted.”
The survey also suggested input prices continued to increase rapidly in June, with the pace of inflation ticking higher.
Around one-third of respondents registered an increase in input costs, again often linked to higher wages and the rise in National Insurance contributions.
“Companies are still confident about the year-ahead outlook, however, so we will hopefully see some demand and output improvements during the second half of the year,” Mr Burnside said.