"I deeply regret any offence caused to any of the many Australians affected by the terrible bushfires by my taking leave with family at this time," Morrison said in a statement Friday.
He added he would be returning to Australia as soon as possible "given the most recent tragic events", referring to the deaths of the two firefighters.
Geoffrey Keating, 32, and Andrew O'Dwyer, 36 died when a tree damaged their truck on Thursday as they battled out-of-control blazes south of Sydney.
Three other firefighters in the vehicle survived with minor injuries.
Criticism of Morrison's absence has been widespread, sparking street protests and a flood of angry social media posts demanding WhereIsScomo.
The situation was worsened by the prime minister's office initially refusing to confirm his whereabouts.
"We are seeing an absolute lack of leadership from this government and it is a disgrace," said Leighton Drury, a firefighters' union leader addressing Morrison's absence, "where the bloody hell are you?"