The 125-page booklet, classified "In Confidence" and containing the phone numbers and contact details of senior personnel from Australia and the US, was found near parliament on Thursday by a Fairfax journalist.
"The incident is currently being investigated," a spokesman for Attorney-General Robert McClelland said.
"In line with long standing practice, the Australian Government does not comment on security matters," he added.
Most of the manual was devoted to a minute-by-minute schedule of Obama's movements during his 27-hour visit to Canberra and Darwin last week, even detailing which car door he would use and the seating arrangements within his convoys.
It also ran through the exact breakdown of his secret service detail and motorcade arrangements, including Obama's ambulance, counter-assault teams, communications and intelligence, according to the journalist, Dylan Welch.
The booklet cover stated that the information was "not to be communicated either directly or indirectly to any person not authorised to receive it", Welch said, and it included contact details for a range of figures.
It also named a long-serving member responsible for Obama's protection.
Welch claimed to have found it in a gutter 100 metres from Parliament House on Thursday.
During his Australia tour, Obama addressed a joint sitting of the nation's lawmakers there that morning, before heading to Darwin to address troops.