The obstruction had caused Rufus to quickly fall ill - which resulted in him showing signs of nausea, vomiting and pain.
"Rufus died due to complications caused by the ingestion and lodgement of the stone."
It was not the first time Rufus had swallowed a stone, Mr Fergus said.
"He has eaten them before."
On the past occasions Rufus had recovered.
"The most likely source is that someone has thrown it in from the beach," Mr Fergus said, adding that staff regularly checked for stones in the enclosure areas.
There were no small rocks and stones inside the Marineland area.
He said the enclosures had been set up in a way to prevent the animals being hit as there had been evidence some people had purposely thrown stones at them.
A post mortem examination was also been carried out on Makea, a 22-year-old sea lion, and father of Rufus, who died on January 11 a few days after falling ill.
The animal had failed to recover from anaesthetic that had been given to him by veterinarians from Massey University who were called in to check him out.
The results of that post mortem had not yet been released.
Two California sea lions and seven fur seals are still being cared for at Marineland while their long-term future is decided on.
Napier City Council officers met with Department of Conservation staff earlier this week as part of a series of regular meetings to discuss a series of options for the seals.
Nothing firm had been decided at this stage.