The Buccleuch Estates posted a £573,000 pre-tax loss for the year ended October 31, according to accounts filed with Companies House, as a miner using its land collapsed and the company put other energy schemes on hold.
Buccleuch had made £1.9m profit in its 2012 financial year, and a £1.5m profit in 2011. This had been a respite after the company racked up losses totalling £30m in the three years to October 2010 due to the property downturn.
Writing in Buccleuch Estates' accounts, the Duke said there had been "considerable progress" within the business, highlighting a post-tax profit of £31,000 for the latest financial year.
In a strategy developed two years ago Buccleuch has focused its interests on property, energy and hospitality and tourism.
However, the impact of shale gas exploitation in the United States, which has sent coal prices tumbling has been felt in the Buccleuch estates in Scotland.
The Duke said: "Energy markets remained volatile in 2013 and UK energy policy continues to be very unclear and ambiguous.
"Coal prices continued to fall due to cheap exports from the US and South America, in turn prompted by the rapid expansion of unconventional gas in the US, which has led many generators to convert to gas, leaving large volumes of US coal looking for export markets."
The consequence of this has been far reaching in the UK and for Scotland in particular; with both Scottish Resources Group and ATH Mining going into receivership in Scotland.
Buccleuch, whose non-executive directors including Tesco Bank chief executive Benny Higgins, estimated that this has left the country with £160 million of uninsured restoration liabilities "as well as devastated local economies which depend on these activities for employment".
Buccleuch's Queensberry Estate owned the site of Glenmuckloch coal mine whose operator ATH Resources went into administration at the end of 2012.
Buccleuch has formed a joint venture with Hargreaves Surface Mining to retrieve more coal from the site in Dumfries and Galloway, and restore it.
Selkirk-based Buccleuch said its plans to develop a coal mine on the Eskdale and Liddelsdale Estates in the Borders with Kier Mining remains at an exploratory stage "due to current coal pricing".
Similarly, its attempt to extract coalbed methane in partnership with Dart Energy have not progressed.
There have been worries about the impact of hydraulic fracking techniques on the local environment.
The Duke said: "We continue to work with community representatives and government, at local and national level, to address environmental concerns and, for the sake of clarity, until such time as those concerns have been addressed, it is not our intention to use hydraulic fracking.
"We remain convinced, however, that subject to further test drilling, this represents a significant economic development opportunity for Scotland."
Commercial property, the biggest single driver of profit for the group, was more positive.
The Duke said that confidence has begun to return to the property market.
This allowed Buccleuch to achieve better than targeted gains on its investment portfolio.
It disposed of a number of developments including the Evolution site on Glasgow's Oswald Street to German hotelier, Motel One.
On the tourism , side it said visitor numbers across its four estates were up during the year "but remain modest".