The National Day Nurseries Association's annual survey found that private and voluntary childcare providers in Wales are losing on average £863 a year on funded places for three- and four-year-olds.
Extra costs such as the new National Living Wage and the phasing in of pension auto-enrolment are other areas of concern, and business rates and VAT continue to push up costs.
Fees are predicted to rise in 80 per cent of Welsh settings.
The NLW will also hit nurseries in Wales harder than England and Scotland, according to National Day Nurseries Association's other country-wide surveys.
It will push pay up by 13 per cent this year, and have the knock-on effect of a large proportion of settings employing staff under 25.
Occupancy is reducing every year and is down to 67 per cent on average, leading to a loss in business confidence.
Just under a third of nurseries expect to make a profit this year (32 per cent), compared to 55 per cent last year.
Nurseries in Wales are paid the lowest rates for offering funded places for three- and four-year-old places in the UK, at £3.13 an hour, compared to an average of £3.83 per hour in England.
Tories pledge 30-hour expansion
The Conservatives are the latest political party to pledge to increase free hours, announcing today that they will treble free childcare in Wales from ten to 30 hours a week if they win the Assembly elections.
Welsh Shadow Education Minister, Angela Burns AM, will announce today that a Welsh Conservative Government would increase free childcare provision for three- and four-year-olds to 30 hours per week.
'Welsh Conservatives will work towards trebling free childcare for working parents to help parents return to work so they can provide for their family and help deliver a stronger economy,' she said.
Their pledge follows that of Welsh Labour (30 hours over 48 weeks a year) and Plaid Cymru (39 weeks).
However, the NDNA warns that fewer than half of nurseries in their survey would expand provision to offer these hours, amid increasing uncertainty over continuing to offer free places at the current level.
Just over a third of PVI nurseries in Wales are providing childcare places, but choice for parents is limited as local authorities restrict the settings that can offer funded places, and in some areas parents can only use funded places offered by maintained nurseries and schools.
However, a quarter of nurseries do not offer funded places due to poor funding levels.
Less than half of PVI settings in Wales are commissioned by local authorities to offer funded Foundation Phase places for three- and four-year-olds and only a third offer Flying Start places for disadvantaged two-year-olds.
Pre-school children in Wales move between several settings during the day. Typically, a three-year-old could start nursery at 8am, go to school at 9 am for a free place and then at 11.30 move to afternoon provision.
One nursery owner taking part in the survey said, ‘I would like to be able to deliver funded hours, however our authority will not allow flexibility and have limited it to school nurseries and a handful of playgroups.’
Others said they are not given the option to offer free places.
NDNA chief executive Purnima Tanuku, said, ‘The sector is seriously struggling to remain sustainable.
‘Nurseries want to pay their deserving staff more for their hard work but are struggling to afford the National Living Wage which will mean payroll costs rising by 13 per cent this year and by 35 per cent by 2019.
‘This, coupled with chronic underfunding for free places and declining numbers of children attending, is causing real problems.’
Ahead of the Welsh Assembly elections on 5 May, NDNA has launched a childcare challenge for the next Welsh government to make a difference to the choice, quality and cost of childcare in Wales.
Ms Tanuku added, ‘We are calling on everyone interested in childcare to make their vote count and really think about the options on 5 May.’