According to PUNCH, the victims were part of a crowd that struggled to see Joshua during a special healing service on Saturday.
Reports of the Synagogue tragedy became public after 27 persons were killed at Reigners Bible Church, Uyo, Akwa Ibom state.
The building of the church collapsed, an incident to the one which happened at Synagogue in 2014.
At least 115 people – mostly foreigners – were killed in the tragedy.
PUNCH identified two of the victims of the latest unfortunate incident in the church as Emeka Okonkwo and Emmanuel Oherin.
The newspaper said the third victim had yet to be identified.
Their corpses were said to have been deposited in a morgue in the state.
PUNCH quoted a witness as saying the stampede occurred around 4.30am.
“It was the church’s annual deliverance and healing programme. Usually at this time, the church becomes a beehive of activities as people come in their thousands to see the prophet for miracles,” the witness said.
“People lodge in different hotels surrounding the church. And they all arrive at the church very early. There is a canopy on the premises where worshippers are screened before they see the man of God.
“However, on Saturday, after being screened, the crowd was much and they started struggling through the doorway to see the prophet. In the process, three people collapsed. They were rushed to the Isolo General Hospital, where they were confirmed dead.”
Dolapo Badmos, police public relations officer (PPRO) in Lagos, confirmed the incident, adding that investigations were ongoing.