The government has pledged to increase paid-for nursery places from the current 600 hours to 1,140 for three and four-year-olds, and eligible two-year-olds, by August 2020 - equivalent to about 30 hours a week in term time.
The Accounts Commission report said there is a danger that Scotland’s councils will not be unable to meet the increase in provision within the timescale set out by the government.
The commission found: “There are significant risks that councils will not be able to expand funded early learning and childcare (ELC) to 1,140 hours by 2020.
“In particular it will be difficult to increase the infrastructure and workforce to the levels required, in the limited time available.
“The Scottish Government should have started detailed planning with councils earlier, given the scale of the changes required.”
The Scottish Government’s pledge to increase free childcare is intended to help parents work, study or train but some who were surveyed for the report said the measure would have a limited impact on their working lives.
Iain Gray, Scottish Labour’s education spokesman, said the watchdog’s findings “blow a £160 million black hole in a flagship SNP policy”.
Liz Smith, MSP, Scottish Conservative shadow education secretary, described it as “a very serious wake-up call for the SNP”.
And Sheila Thomson of the Scottish Liberal Democrats said “there is not enough juice in the tank” for local authorities.
The report said it would be difficult to increase infrastructure and workforce in the limited time available and that the Scottish Government should have started detailed planning with councils at an earlier date.
It also found council and government estimates of funding and workforce differ significantly with councils expecting day-to-day spending on the scheme to hit £1 billion by 2021-22, compared to the government figure of £840m.
Local authorities estimate they will need 12,000 whole-time equivalent (WTE) staff by the same time while the government believes between 6,000 and 8,000 WTE staff will be needed by 2020. Councils expect to spend about £690m for changes to infrastructure by 2021-22, higher than the £400m Scottish Government figure.
The report also examined the 2014 expansion of funded places to 600 hours and found the government had invested almost £650m but did not plan how to evaluate this meaning “it is not yet clear whether the investment is delivering value for money”.
Auditors also criticised agreeing the expansion without examining other options or having evidence it would achieve desired outcomes.
Accounts Commission chairman Graham Sharp said: “The scale of change needed over the next two years is considerable and there are significant risks that councils will be unable to deliver that change in the time available.
“There is now an urgent need for plans addressing increases in the childcare workforce and changes to premises to be finalised and put in place.”
Stephen McCabe, spokesman for children and young people at the Convention of Scottish Local Authorities (Cosla), said: “We will focus on delivering the expansion of ELC with our partners, taking the necessary time to ensure our focus remains on the high quality education of young children.”
Maree Todd, minister for childcare and early years, said: “It is not unusual, at this point in the life of a major project, for people to have different ideas as to the final cost.
“That’s why we are working with councils to help them develop their expansion plans and have recently reached agreement with Cosla on the process of arriving at the multi-year funding needed.
“I look forward to many more children and their families benefitting from high quality, funded early learning and childcare as we work towards successful delivery of expansion.”