Though the overall cost of Australia's first such programme for international routes was not disclosed, Justice Minister Chris Ellison said Australia's government would contribute at least A$10 million ($7.4 million) a year.
"Now that we've got the agreement with Singapore and finalised the details with Qantas, the programme's up and running as of today," Ellison said.
He said similar air security deals were being negotiated with the United States and Canada. Discussions with other countries would begin as risk assessments were carried out.
"I'd hope to have an agreement with the United States early in the New Year," he told Sky Television.
Australia and Singapore agreed on the aviation security deal. Ellison has described the air route to and from Singapore as one of Australia's busiest with more than 12,000 flights a year by Qantas and Singapore Airlines.
No fare increase
Ellison gave no indication of whether Singapore Airlines had begun using guards on its Australian routes.
Qantas chief executive Geoff Dixon said he did not expect fares to rise as a result of the security deal.
Australia began putting armed guards on randomly chosen domestic flights two years ago after the September 11 hijacked airliner attacks on the United States.