The company has deferred next year's basic salary reviews for six months, blaming the continual economic downturn, it has been reported by The Guardian.
Last month Trinity did the same thing, while both companies reported a significant downturn in the advertising market in November.
Tim Bowdler, chief executive officer at Johnston Press, said: "This decision is necessary to help safeguard the future of our companies.
"In six months time, we hope our operating companies will be in a better position to determine the impact of the recession and to decide whether or not a salary increase can be afforded.
"Over the next few weeks, our company managing directors will be holding meetings with our employees and trade union representatives to explain the decision and discuss how it impacts local agreements."
Unite national officer Steve Sibbald said that he expected its members at the company to be angry in light of the "huge profits Johnston Press has made in recent years".
He added that Johnston Press was difficult to work with on its deferrals because it owned many companies with differing agreements.
He said: "In some sites they have a two-year agreement in place so effectively they won't be honouring those agreements. In the Republic of Ireland there are labour laws that they will have to adhere to.
"Some sites aren't even due pay reviews until after the six months anyway. Because there are so many sites it is quite difficult, there is a massive difference in obligation from site to site."
Johnston Press latest to freeze staff pay
Local newspaper publisher Johnston Press has followed Trinity Mirror in announcing that staff pay will be frozen in the early part of 2009.