A customs officer at Sydney international airport confiscated a mobile phone from a passenger during a baggage search and then secretly used it to send and receive messages without the passenger's knowledge.

The November incident has been referred to the Australian Federal Police, but the new Department of Immigration and Border Protection has refused to release further details, prompting widespread concern and a call for a federal police investigation into the actions of the customs officer.

The illegal use of a traveller's phone has been referred to the AFP.

The passenger, a 22-year-old man who did not wish to be identified, discovered what had happened only when he received a letter from the Integrity and Professional Standards branch of the department, saying it was investigating the "inappropriate use" of his phone by the customs officer.

The letter dated nearly six months later, said "this behaviour does not uphold the standards expected of our officers at the border and on behalf of the department and the ACBPS [Australian Customs and Border Protection Service] I apologise that it occurred. The letter said the "appropriate steps" were being taken in relation to the incident.