The freeze will affect all of the group's UK and Ireland employees until early 2013. It follows back to back pay rises in 2010 and 2011.
Staff received an email last week informing them of the pay freeze but that they would receive an extra day's leave in 2012 in lieu of a pay review.
The company has reassured staff that they will benefit from a 2% pay pay rise in 2013 if profit forecasts for the current financial year are met.
Commenting on the pay freeze, Unite national officer Steve Sibbald said: "I suspect members will keep their heads down in light of the precarious state of the company."
The announcement comes a week after News International terminated its contract with Johnston Press for £30m to end its 15-year contract with Johnston Press just five years into the agreement.
Johnston Press human resources director Malcolm Vickers assured PrintWeek that no cuts to headcount would be made as a result of the News International contract termination. The company was confident that it could fill the "premium-quality" equipment used for the News International work, he confirmed.
However, Sibbald said: "The News International contract kept Johnston Press’ Portsmouth and Dinnington plants running.
"When News of the World closed, it wiped out a shifts’-worth of work."
But he added: "Vickers assures me that Johnston Press has a few irons in the fire and potential contracts to fill those presses."
For Johnston Press, 2012 has seen a number of consolidations: it announced that its five daily publications were to become weeklies, and later closed one of those five, the Peterborough Telegraph.
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