Permission was granted in September to convert an existing steading to create the house, including a zen garden, hot tub and cinema room, at Culchunaig.
Councillors at Highland Council's south planning committee approved the plans.
The site sits around 50 metres from the south west boundary fence of the National Trust for Scotland section of the battlefield and visitor centre.
Now, the Scottish Government's Planning and Environmental Appeals Division has "called in" the application for the house, and will decide itself whether it can be built or not.
One councillor described the move as "genuinely fantastic news" given ongoing concerns surrounding development in the Culloden area.
Highland Council was notified of the direction by letter from the division.
It said: "Scottish Ministers have given this Direction in view of the proposed developments potential impact on Culloden Battlefield, which is a nationally important battlefield."
The government's intervention comes amid growing concern that land within the historic boundary of the battlefield is not being fully protected from development. A conservation area set up around the site has so far had little impact.
The National Trust for Scotland site represents only around one third of the battlefield area, with the remainder in private hands and therefore vulnerable to development proposals.
A development to build 16 homes at Viewhill Farm, which sits on the fringes of the historic battlefield boundary, is almost complete. It is understood another four applications relating to the battlefield site are going through the planning process.
Plans to build on the Culchunaig site were described by the Historians Council of Culloden as an "appalling intrusion of a national war grave" with evidence that it had a "major role" in the April 1746 battle between the Jacobites and British Army.
Permission to build at Culchunaig was granted originally in 2015 with the recent application an amendment to the original proposal.
Councillor Andrew Jarvie (Conservative), a member of the South Planning Committee, welcomed the Scottish Government plans to call in the application.
He said: "This is genuinely fantastic news that the Scottish Government are finally using their powers to protect our Country's most important heritage sites.
"This application made a complete mockery of the Conservation Area, this is a large home on the boundary fence of the battlefield visitor site and 500m direct site from the visitor centre itself.
"When this came to committee, we had no other decision to make because under Scottish Planning Policy, the previous grant of planning permission set the precedent of development being acceptable on this site.
"This previous permission was made under delegated powers and Councillors did not even get a say on it. So when this came to committee, it was no more than a formality.
"At the committee, I made it clear my intention, along with Ward colleague Carolyn Caddick, was to refuse planning permission. However our hands were tied by the previous officer decision, a refusal would have inevitably been overturned and the Council billed for unreasonable costs.
"All I can hope is that the Scottish Government see sense and don't allow this inappropriate development to go ahead."
George Kempik, of the Group to Stop Development at Culloden, said the campaign group wrote to the Scottish Government with concerns about how the planning meeting was conducted in September.
He added he was "very encouraged" that the application had now been called in.
Mr Kempik, from Inverness, said: "We got heavily accused of over protection of the Viewhill site as it is on the fringes of the battlefield area but when you look at Culchunaig, this was really in the heart of where the battle took place.
"Historic Environment Scotland did nothing to stop this application. The fact that the Scottish Government will now look at it encourages us massively.
"There is massive public support against development at Culloden and it is not just about locals, about Inverness. When they look at any application for development on this historic battlefield, they have to think of all the people all over the world who are fighting to protect this place."