Profits were $46.3m (£32m) or 30 cents a share, down from $63 (£43.5m) or 37 cents a share last time. Analyst forecasts were between 20 cents and 35 cents a share.
Third-quarter advertising fell 14.5% across the group as a result of tough market conditions and the affects of the terrorist attacks.
Third-quarter advertising revenues at the New York Times newspaper fell 14.4% to $236m (£162.9m). At its New England Newspapers division, home to the Boston Globe, third-quarter revenues fell 21.2% to $102m (£70.4m), while the Boston Globe itself saw revenues climb 5%.
The company said the decline in national ad revenues was largely down to softer technology, travel and e-commerce advertising.
Classified advertising revenues continues to be hurt by a decline in recruitment advertising. However, this was offset by an increase in property ads and automotive ads.
Shares in the New York Times Co climbed 0.5% to $42.21 (£29.10).
Last month, the New York Times Co followed Dow Jones, publisher of the Wall Street Journal, in issuing a warning that its results would be worse than expected.
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