BBC Scotland reported that three months after a new round of funding for the Help to Buy scheme began, all the cash for the central area of Scotland has already been allocated.
A total of £275 million had been pumped into the scheme, which provides financial assistance for those buying a new build property, by Holyrood ministers.
Demand has been "extremely high", the Scottish Government said, with more than 2,000 homes purchased so far using the initiative.
Homes for Scotland, which represents the housebuilding industry, said it was "frustrated but not surprised" by reports that funds for the scheme for this year are almost fully committed.
Tory housing spokesman Alex Johnstone claimed: "Because of mismanagement of Help to Buy by SNP ministers there are real fears that people hoping to own their own home may lose out."
Help to Buy allows both first-time buyers and existing homeowners buying a new-build house from a participating builder to get up to 20% of their purchase price.
The Scottish Government then takes out an equity stake in the property, which the buyer has to repay at a later date.
Homes for Scotland chief executive Philip Hogg said: "Having worked closely with the Scottish Government on monitoring of the Help to Buy (Scotland) scheme since its launch last September, we are frustrated but not surprised by this news.
"Quickly aware of the high level of interest, we have consistently called for additional budget to ensure the scheme can meet the demand which clearly exists. This is demonstrated by the fact that it has already generated some 3,500 sales and reservations."
He added: "Without a doubt, the Help to Buy (Scotland) scheme has proved a huge boost, not only in terms of stimulating the building of much needed new homes but also in supporting jobs and wider economic recovery.
"Whilst the scheme will remain in operation with £100 million allocated for 2015/16 to support buyers across Scotland, any interruption now will obviously be hugely frustrating for both buyers and builders alike.
"With Westminster having pledged support for the English scheme until 2020, we will continue to work closely with the Scottish Government on the development of a longer-term strategy here."
Mr Johnstone said the "popularity of the Help to Buy scheme should have come as no surprise to the Scottish Government" as Westminster's economic policies had created jobs and "given people in Scotland the confidence to go back into the housing market".
But he said the Scottish Government "should have not been signing off mortgage applications without first knowing enough funds were in place to honour agreements with those applying to the scheme".
A Scottish Government spokeswoman insisted all applications that had been approved so far under the scheme would proceed.
She said: "More than 2,000 homes have been purchased through Help to Buy Scotland to date with an additional 2,000 likely to be completed by the end of the financial year. All applications that have so far been approved will proceed.
"Demand for the scheme continues to be extremely high and ministers have already allocated an additional £50 million to the scheme this year, taking total funding to £275 million. We are also actively considering how further demand can be supported in this financial year.
"In the meantime, if people who have not yet had an application approved are considering buying a house through the scheme, they should in the first instance contact the agents managing the scheme to check availability."
But James Kelly, Labour's infrastructure spokesman, said: "We know lots of young people and families are unable to get their own home and this huge shortfall just highlights the high demand there is for affordable housing in Scotland.
"We have been urging the SNP Government to come forward with an action plan to deal with the pressing need for affordable housing and unless we bring real focus to this area many people will be left in unaffordable or inappropriate housing."