Duncan Taylor Scotch Whisky Limited said it had used the name of the famous monster-containing loch since 2008 and wanted trademarks owned by another firm, Loch Ness Spirits Limited, cancelled.
However, the Intellectual Property Office rejected its claim, saying that the business could not prove it was the owner of any "goodwill" generated under the name Loch Ness.
It also ordered Duncan Taylor Scotch Whisky - which is the owner of one of the largest privately-held collections of Scotch whisky casks - to pay Loch Ness Spirits's costs of £3200.
Duncan Taylor said it had moved away from brokering of whisky in cask form to focus on the production of the spirit in 2008, when it began making Loch Ness Whisky in May 2008.
Loch Ness Spirits argued that Loch Ness was a "well-known place in Scotland" and that the name of the loch should be "taken as an indication of geographical origin (rather than the trade origin) of spirits".
"[It] is therefore not a distinctive mark for such goods," it said.
Hearing officer Allan James added that the "most dominant and memorable" element of the company's labelling was a "monstrous creature" - Loch Ness Monster - rather than the words Loch Ness.
He said: "I conclude that the applicant has not shown that it is the owner of any goodwill generated under the name LOCH NESS in relation to whisky. This is sufficient reason to reject the applications on this basis alone."