Canberra and Goulburn Archbishop Christopher Prowse said he felt the need to speak out after the loss of conditions which could result in wage cuts of 20 per cent after last week's shredding of guidelines covering many cleaners at Commonwealth buildings.

"There’s a moral dimension here, and I think as a religious leader I need to raise my voice and blow the whistle and say, ‘Hang on. In the rush to make Australia better I think we’re, in this particular case, forgetting about a very important group of our workers'," Archbishop Prowse said.

"They're the new Aussie battlers, because most of them are coming from overseas. They generally are some of the lowest-paid workers in Australia, the ones that do the hidden work for us, they come to work when we’ve gone home."

The removal of the cleaning services guidelines for Commonwealth government tenders, first put in place by Labor in 2011, is set to cost full-time workers at least $370 a fortnight if pay levels drop to modern award rates in future contracts.

Appointed in September, the head of the region's Catholics met with United Voice union members on Friday and said they were "desperately let down" by the erosion of their conditions, and there was a need to be careful that the "noble aim" of balancing the budget was not reached by using people as fodder.

Asked about Jesus' biblical direction to a group of soldiers to "not complain about your wages", Archbishop Prowse said economic matters could not be ignored.

"Jesus said don’t be obsessed with your wages, he didn’t say they’re not important."

Liza Grealy, who cleans a federal government building in Civic, said the loss of $370 a fortnight would stop her driving to work.

"I'm in a housing commission home now, it's going to be very, very hard," she said.

Employment Minister Eric Abetz, an Anglican, has criticised the "ad hoc" nature of the guidelines, which apply to at least 1000 workers in Canberra and to federal CBD buildings nationally.

United Voice ACT secretary Lyndal Ryan said nearly 50 medium to large cleaning companies - a majority of that end of the market - had voluntarily signed up to Clean Start collective agreements providing equivalent conditions in 2012, but the end of the guidelines meant they would need to breach the agreements to compete with those tendering for Commonwealth work at award rates.

An ACT government spokesman confirmed Clean Start wages and conditions would be maintained at territory sites.