Australian Federal Police Commissioner Krissy Barrett revealed the assessment on Tuesday, citing an initial finding by the Philippine National Police.
The pair is known to have arrived in the capital, Manila, from Australia on November 1 before travelling on to Davao City.
They arrived back in Sydney on November 29, two weeks before the shooting attack at Bondi Beach that left 15 people dead and scores more injured.
"The initial assessment ... is that the individuals rarely left their hotel, and there is no evidence to suggest they received training or underwent logistical preparation for their alleged attack," Ms Barrett said.
"CCTV footage capturing their stay in the Philippines has been provided to the AFP, and we are currently reviewing that material.
"What this points to - and I will again advise this is a point in time assessment - is that these individuals are alleged to have acted alone."
Ms Barrett was giving an update on Operation Arques, the ongoing counter-terrorism investigation into the December 14 attack by NSW Police, Australian Federal Police, the Australian Security Intelligence Organisation and the NSW Crime Commission.