In a statement, the union claims staff who crossed the picket line were given a bonus of two days pay. The union said if this pay had been evenly distributed amongst staff "it is likely that the dispute would already be over".
Editor in chief of the Southern Daily Echo Ian Murray told Journalism.co.uk that staff who worked during the two periods of industrial action carried out extra duties and covered extra hours, which has been "recognised".
"As such not everyone received the same payment," he said in a statement.
"I am surprised that the NUJ would not wish for journalists to be recompensed for their efforts.
"To suggest that staff not in work should receive part of the payments due to those who did carry out extra duties is patently absurd."
Staff at the Southampton-based paper went on strike for two days on 9 and 10 November over an ongoing pay freeze.
The union then cancelled another 48-hour strike to arrange a meeting with management, but with the dispute remaining unsettled a further two-day strike was held on 7 and 8 December.
According to the NUJ around 40 of its members, which represents roughly 75 per cent of editorial staff at the Echo, took part in the most recent strike action.
The union claims that some members of staff who did not take part in the dispute have said that they are "uncomfortable" with taking the bonus and as such the chapel has invited them to donate the money to its strike fund.
In his statement Ian Murrary said that he "fully understood" if staff wanted to donate their extra payments to charity.
"That is their choice," he added.
Ballots for industrial action have been held at a number of other Newsquest-owned titles in relation to the ongoing pay freeze, redundancies and in the case of the Brighton chapel, the relocation of its subbing operations to Southampton.
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