Childcare is the classic early intervention service, theoretically the ideal chance to provide struggling families and at-risk children with help, in a way parents are likely to accept.

It's also a key factor in the UK Government's attempts to encourage people back into the workforce, and a major plank of the Children and Young People Bill which the Scottish Government is keen to pass ahead of the independence referendum.

So a report this week which warned of significant variations in the cost of care across Scotland and gaps in provision goes to the heart of several social policy agendas.

The study by the Family and Childcare Trust (FACT) and Children in Scotland (CIS) found the price of nursery care appears to have stabilised, which is good news as the annual survey had shown prices rising alarmingly in previous years, according to CIS.

Out-of-school care, such as after-school clubs and breakfast clubs, continue to become more costly, however.

The report also criticised local authorities, claiming 40% of councils do not know if they have enough childcare for working parents. Only 20% of councils said they definitely did, and just 25% were sure they had enough for five to 11-year-olds.

Councils taking part in the survey were promised anonymity in return for being frank about gaps in their knowledge and holes in local services.

Nevertheless the body representing Scotland's councils has questioned the findings of the survey, which also claimed after-school clubs cost more in Scotland than in any region of England apart from the north-east.

Cosla president, Councillor David O'Neill, said costly childcare was clearly an issue for families but the quality of what was on offer was also important.

He said: "The survey touches on an important issue, but it unfortunately seems to downplay many of the complex issues that local authorities face. High quality, affordable childcare is hugely beneficial not just to parents wanting to work, but also for the long-term future of their children.

"It is worth emphasising that the survey appears only to look at childcare provided outwith the formal pre-school that all three and four-years-olds are entitled to."

He said it was also true that childcare can take many different forms and added: "It is not immediately apparent from the survey how the comparisons have been made, and the figures calculated."

Local councils have a vital role in ensuring childcare is affordable, especially for families from deprived backgrounds in need of support, he argued. But parents will inevitably have to make a financial contribution to the care of their child.

In regard to the report's claims of a postcode lottery in terms of pricing, Mr O'Neill added: "The survey tries to compare Scotland with the north of England. We are always cautious about drawing comparisons between different parts of the UK where education and legal positions can be very different. However, we are not surprised that there is some variation in the cost of childcare – across the Border and within Scotland."

Both variations in the cost of living and the local impact of supply and demand could influence regional variations, he said.

In response to the report's claims that new legislation might be needed to ensure councils address gaps in local provision, Mr O'Neill said Cosla would continue to work with the Scottish Government on the Children and Young People Bill as it makes its way through Parliament.

"Local government is a strong supporter of high-quality early years services, of which childcare is a vital component. The Bill will no doubt stimulate a further debate on the cost of early learning and childcare."

Jim Stephen, CIS policy officer, acknowledged that the formal pre-school care guaranteed for all three and four-year-olds was being delivered. But he added: "Councils have no legal obligation apart from 475 hours, though some local authorities are providing 570 hours of care. The Scottish Government is to spend £78 million in 2014/15, rising to £109m in 2016/7, and that is a huge commitment in financial terms.

"Policy is heading in the right direction and that seems to be backed by money."

CIS would also like to see more vulnerable two-year-olds entitled to care, he said, while more flexible options including affordable after-school care are vital with the increasing prevalence of shift work.

"Services do also need to be good quality. It shouldn't be about herding and minding children. We recognise that care providers have done well to keep costs stable, despite rising energy costs, staff costs and other pressures. There has also been a push to upskill the workforce.

"We need greater flexibility, especially to cope with differing work patterns. Out-of-school care is unregulated, mostly in the private and voluntary sector with no subsidy.

"The thrust north and south of the Border is to have support for parents and carers who are going to return to work."

This is linked to the UK Government's welfare reform agenda, and Mr Stephen said recent "hideously complex" changes to tax credits relating to childcare were worrying. "This is an area that really bothers us, and it is virtually outwith Scottish Government control.

"There is a real catch-22 in communities where people are being urged into work and training to offset benefit cuts, but find childcare too expensive to afford."

One measure in the Children and Young People Bill will require councils to have a childcare plan for their area. FACT has called for them to use this information to intervene to address local market shortages, but it is unclear how this would be paid for.

Mr Stephen added: "The First Minister has promised transformational world class childcare in Scotland. We would say that means it has to be affordable, available, flexible and high quality. It should be laying the foundations for social and educational development and for transition into primary school."

Aileen Campbell, Minister for Children and Young People, said the Scottish Government was determined to make high-quality childcare more affordable for families.

"That's why we're increasing the level of free, flexible and family friendly childcare for three and four-year-olds to at least 600 hours through the Children and Young People Bill. This will save families around £700 a year.

"We want early learning and childcare to be flexible and meet the needs of the local community and parents as set out in the new legislation and we are looking at provision of out-of-school activities and the particular challenges faced in rural areas highlighted in the report."

The First Minister has asked the Council of Economic Advisers (CEA) to consider full economic and social benefits of improving childcare, she said. Children in Scotland has said CEA will be supplied with a copy of its findings.