Mike Benson, director of the attraction, said there was little left to examine of the structure, which went up in flames in June.
Police and fire investigators have ruled out any suspicious circumstances surrounding the blaze, with the events surrounding the fire remaining a mystery.
Mr Benson said a small orange glow was recorded on CCTV footage after 11pm on the night of the fire, with the building gone six minutes later.
He said: “Nobody will probably ever know what started the fire. Six minutes after the orange glow was seen on CCTV, it was gone.
"There is literally nothing left to look at.”
Mr Benson said electricity supply to the Crannog underwent regular checks and that a real fire in the attraction was not lit on the day of the major blaze given the summer weather.
“The main thing is that police and fire [services] ruled out anything suspicious,” he said.
"It could have been an ember in the sky from a barbecue, anything.”
Mr Benson said he had now “stopped crying” following the fire, adding the help and support received in its aftermath had been “humbling … gorgeous”.
The fire led to a huge public response, with a crowdfunder led by local businessman Jonathan Morley raising £50,000. A cheque was presented on Tuesday afternoon to the centre by Mr Morley and a further £30,000 has been raised through other donations.
Earlier this month, the Scottish Government gave the Crannog Centre £51,000 to help the recovery from the fire. The centre re-opened five days after the blaze and continued to offer its summer programme of events.
Plans to build a new centre on the opposite side of the loch at Dalerb, where three crannogs would be built in the water and a replica Iron Age village on the shoreline, are now being accelerated. A meeting is due to be held with Scottish Government officials later this month to discuss funding.
Mr Benson said: “The fire is not the end of our story, it will become part of our story.”
Originally, it is thought there were at least 17 crannogs dotted up and down the water at Loch Tay, with it known people settled on the water from around 370BC.
Built from alder with a life span of around 20 years, the structures simply collapsed into the loch once they had served their purpose.
The crannogs were probably considered high-status sites, which offered good security as well as easy access to trading routes along the Tay and into the North Sea.
It is believed that 20 people and animals lived in a crannog at any one time.
Many trees were used to fashion the homes, with the Iron Age residents having a solid knowledge of trees with their houses thatched with reed and bracken. Hazel was woven into panels to make walls and partitions.