A £194.7m writedown of Johnston Press's 200 titles left their carrying value at £548.8m.
In a rare move, accountant Deloitte highlighted "material uncertainty which may give rise to significant doubt over the group's ability to continue as a going concern".
Johnston Press focused on a 4.3% rise in like-for-like operating profits, excluding writedowns, to £28.6m for the 26 weeks to June 29, its first increase for seven years.
Chief executive Ashley Highfield insisted the warning over Johnston Press's going concern status was "not new news" because the risks around the business had changed little, but was a function of the auditors looking further ahead.
"The auditors are required to look 15 months out and looking at the outer quarters they wish to highlight, and indeed we have highlighted, that were a tsunami of a combination of events to happen we might get closer to our (bank) covenants than we would ideally like," he said. "It is prudent to make people aware of it."
Deloitte highlighted the risks of a deteriorating economy, the company's failure to execute its strategy, shortcomings in cost savings and delays in selling assets which could lead to it breaching the terms of its loan deal.
Johnston Press's shares closed down 0.25p or 1.6% at 15.75p. Nevertheless, many in the City are still optimistic.
Panmure Gordon analyst Alex DeGroote said: "We remain very confident in the (Johnston Press) turnaround story."
Before the latest writedown, Johnston Press previously wrote £163.7m off the value of its titles in 2011 and £109m in 2008.
New finance director David King said the latest writedown brought it in line with market valuations of the sector. He added that his own "new-broom prudent view of growth rates" was also a factor.
During the most recent six-month period Johnston Press also wrote down the value of its printing presses by £57.9m.
Mr Highfield said the City had "shrugged off" the writedowns.
Johnston Press cut 484 jobs over the six month period, including 15 redundancies at the Scotsman and its sister titles, to take staff numbers to 3746. The company employed nearly 6000 people at the beginning of 2011.
Asked about future job cuts, Mr Highfield said: "I do not want to get into staff numbers."
But he added:"We are going to continue our tight control of costs."
This would continue until the growth of its digital activities outweighed any continued decline in print circulation which the former Microsoft and BBC executive said would probably not be until 2016. Johnston Press has struggled under the weight of a debt pile of as much as £700m built up during a series of acquisitions in the run-up to the credit crunch.
Net debt fell during the latest period from £361.7m to £306.4m, helped by the buy-out by News International of its print contract last year.
The company faces interest rates of around 14% and Mr Highfield said the he is keen to approach the bond markets for refinancing in a move he thinks could reduce rates to 8% to 9%.
The way its bank loans are structured means that Johnston Press could benefit to the tune of £25m if it pays them off during 2014.
Total advertising revenues declined 13.6% in the half year but Johnston Press reported a favourable trend with the rate of decline slowing to 6.3% in June and July.
Its digital revenue was up 13.3%, despite being hit by a slow recruitment advertising market.
Mr Highfield said: "It is still tough out there."
But he added: "I think the advertising market will strengthen if the recovery in the economy continues."
Excluding the five daily titles it moved to weekly publication, the group's like-for-like circulation revenues fell 0.7% in the first half.
There are no plans to reduce the publication frequency of the Scotsman, Mr Highfield said.