A project to introduce fingerprint and facial recognition technology across the country has been scrapped, after massive cost blowouts and delays.

The Australian Criminal Intelligence Commission (ACIC) inked a $46 million deal with tech company NEC Australia in 2016 to expand the nation's fingerprint database to include other biometric information, such as facial recognition and footprints.

But the project has been hampered by missed deadlines and overspends of millions of dollars.

"The Australian Criminal Intelligence Commission has decided to discontinue the Biometric Identification Services (BIS) project," ACIC chief executive Mike Phelan said in a statement.

"This decision was taken in light of project delays."

Mr Phelan also confirmed the commission had asked the National Audit Office to investigate the management of the project.

"The ACIC is committed to delivering projects that enhance capability for our law enforcement partners," Mr Phelan said.

"As part of this approach we regularly review the scope, expected benefits and ongoing feasibility of our projects."

NEC Australia said it was "extremely disappointed" by the decision to dump the project, and launched a spirited defence of its work.

"NEC has worked closely with the ACIC to deliver the BIS project and have clearly demonstrated to the ACIC that we already have a high quality solution that will meet their needs," the company said in a statement.

"It is important to note that the ACIC terminated the contract under the 'termination for convenience' clause, and not because NEC had been in breach of its obligations.

"The termination for convenience clause allows government departments and agencies to terminate a contract, regardless of whether or not the contractor has committed a default or breach of that contract."

NEC said it had a strong reputation around the world for its work in biometrics.

The Federal Government has continually spruiked its aim to become a world leader in digital transformation, but the Opposition has pointed to this project as being just one example among many of serious failures in administration.