"They believe a major issue was a ventilation shaft which was open, which would've allowed water into the engine room when the submarine dived," Mr Sumption said.
The 55 metre-long submarine was patrolling the waters off Papua New Guinea at the outbreak of World War I, helping the Australian navy capture the German Pacific colonies.
Researchers believe it was cruising the surface near the Duke of York Islands on September 14, 1914.
It had a ventilation valve open, possibly to make the tropical conditions a little more bearable for the crew.
The hypothesis is the commander believed there was time for a practice dive and when the submarine went below water, the ventilation valve was left open.
Mr Sumption said it's a possibility, but they'll never know for sure.
"We really don't know and I don't think we'll ever know why that valve was open. This is very embryonic technology. This is very much first generation, mass produced submarine technology. It's very likely it could have been an engineering or industrial failure," he said.
There was rapid flooding and a complete loss of control when AE1 went underwater.
The submarine sank below 100 metres and imploded; the crush killing everyone instantly.
At the War Memorial in Canberra on Friday, mourners commemorated the service of the submarine and its crew on the 104th anniversary of its sinking.
The Navy's director-general of submarine program, Commodore Tim Brown, said those on board were extraordinarily courageous.
"Their bravery is unquestioned. For us, who know infinitely more about submarines today and the undersea domain than was the case in 1914, the mettle and resolution of our forebears is astonishing," Mr Brown said.
It's likely that at least some human remains are still inside the submarine.
The steel hull is eroding quickly and only parts of AE1 are expected to still be visible over the next few decades.
Researchers are calling on the Australian government to train Papuans to protect the site, now a tomb for 35 submariners.