A new deal will see some Department of Home Affairs staff receive a 7 per cent pay rise, nearly five years after their last increase.

The Fair Work Commission (FWC) has interceded after negotiations on a new bargaining agreement for the department's immigration and customs employees failed.

The Commission ordered the department to issue an immediate pay rise of 4 per cent, followed by a further increase of 3 per cent next year.

“We are … very mindful that employees who were covered by the former … agreements have not had a wage increase (excluding salary advancement related increases) since July 2013 … almost five years ago,” the FWC’s statement read.

CPSU National Secretary Nadine Flood said more than 13,000 Home Affairs staff would welcome the ruling.

“[But] it's pretty tough that they won't get backpay to pay the bills that have been stacking up for five long years,” she said.

Ms Flood said the failed talks are a clear indictment of the Federal Government's bargaining policy.

“They have kept fighting right up until now to stop Home Affairs workers and other public servants just keeping their current rights and conditions,” she said.