Islanders on North Uist are behind the plans for the 1.8MW project in Clachan, which is expected to cost £2.7 million but will generate a "significant" amount of money for the wider community in the years after it is built.
The MoD had earlier objected to the scheme, and officials at Western Isles Council had recommended the project be rejected, but the island council's environment committee voted in favour last month.
However, ministers have now called in the plan and it will be considered by a reporter before a further decision is taken.
Residents claim the delay to the project will cost the community at least £1.5m and say it is a blow when their population is now less than 1500 and still dropping.
Robert Fraser, chairman of the community-led North Uist Development Company (NUDC) which has a membership of 500, is behind the project. He said: "There is huge local support for the project here."
Under the plans, the turbines would be 100% community owned and it had been calculated that for the first 15 years, while loans were being paid off, they would generate more than £200,000 a year for the community. This would rise to £485,000 a year for the last five years.
"That sort of money coming would make an enormous difference," Mr Fraser said.
The turbines were among four developments approved by Western Isles Council against advice from their own planning officials and in the face of objections from the MoD, which had objected on the basis the wind turbines would cause interference to the radars on North Uist, South Uist and St Kilda connected to the Hebrides Rocket Range.
After the decision by councillors, the MoD said it "works hard to balance its support for the government's renewable energy policies and targets with its responsibility to ensure that military operations are safe and that defence interests are not adversely affected by wind turbine developments", adding: "Each wind turbine planning application is assessed on a case-by-case basis and on its merits."
However, Mr Fraser said yesterday: "This call-in means considerable delay, which in itself is a major problem for us because it is widely reported the feed-in tariff (paid to developers for the electricity generated), is going to drop by up to 20%. What we had been trying to do was to get our scheme pre-registered, which would have given us a year to put the turbines up.
"Under the current arrangements we would have had £5.5m over the life of the project. That is now likely to drop now to £3.935m. So it is a million-and-a-half of a loss."
He said that because the MoD had been objecting, the NUDC had sought advice from highly qualified consultants, who did not agree with the MoD's positions.
He said the last thing NUDC wanted to do was jeopardise the Hebrides Range, because it is vital to the islands' economy, so it had contacted the range in 2010 when it was considering a single but much larger turbine. "At that point the MoD said they had no objection to developing this site," he said.
A spokeswoman for the Scottish Government said: "Ministers called in the planning application for two wind turbines at Locheport, North Uist because of the proposal's potential for unacceptable interference to the range control radar(s) on South Uist and St Kilda. A reporter will now be appointed by ministers to examine the case and prepare a report for ministers' consideration."