The survey by parent campaign group Fair Funding for Our Kids (FFFOK) suggests 1,081 children in West Lothian and Glasgow alone are unable to take up their 600 hours a year of free childcare.
FFFOK delivered the figures, which are based upon responses from nursery providers, to the First Minister Nicola Sturgeon and education secretary Angela Constance yesterday.
Their survey is in response to what they see as the Scottish Government's failure to recognise that a large number of children are missing out on the funded hours because the majority of places are available at council-run settings.
It will now be sent to nurseries across Scotland in a bid to find out how many children attend partnership nurseries without funding.
According to the 47 out of 95 partnership nurseries in Glasgow that responded to the survey, of the 1,608 eligible children attending their settings, only 873 are able to take-up the funding. This leaves 743 children having to pay for their place.
In West Lothian, responses from 18 out of 23 nurseries indicate that of the 673 eligible children attending the settings, 338 are without a funded place.
This is despite the first minister and education secretary repeatedly claiming 98.5 per cent have registered for the places.
However FFFOK claims the registration figure doesn’t measure whether children are getting a free place and is in effect meaningless as a way of assessing the success of the policy.
The registration figure is thought to include children who have yet to receive a funded place and children with a place at a partnership nursery without funding, as well as counting children more than once if they are on more than one list.
FFFOK will now send the survey to nurseries across Scotland in a bid to find out how many children attend partnership nurseries without funding.
In January, FFFOK met the first minister and asked that she appoint someone to audit delivery of the policy so far. The parent campaign group says she initially declined to do so, but has now said that she will ask the national statistician to look at how data is collected.
Jenny Gorevan of FFFOK Glasgow said, ‘There is a great deal of smoke and mirrors around what the Scottish Government says about the free nursery policy. Our concern is that no-one is on top of how it is being delivered.
‘We have been campaigning for a year and nothing has happened. There are now children who will start school having missed out on all the funding they were ever going to get.
‘We will be asking the First Minister to take immediate action to ensure the money she has promised makes it to the frontline and we will be asking Angela Constance to get on top of how the policy is working in practice. The most basic start would be to get a definitive number of how many children are missing out then we would gladly work with her on how to fix it.’
A Scottish Government spokesperson said, 'The Scottish Government is fully funding local authorities for the additional costs of this policy, based on figures agreed with COSLA (Convention of Scottish Local Authorities). This funding increases annually to enable local authorities to increase flexibility and choices for parents.
'It is for local authorities to manage their own budgets and to allocate funding on the basis of local needs and priorities. However, local authorities must fulfil their statutory obligations to secure adequate high quality childcare provision in their areas.
'While we are not aware of any situation where a local authority is unable to meet its statutory obligations, we have agreed to look more closely at how we monitor and evaluate implementation of the policy.'