A Nigerian official told the BBC the bodies of 1,075 victims had been taken to mortuaries in the city of Jeddah – higher than the official toll of 769.
Other countries also said they had been sent the photos of some 1,090 bodies.
But the Saudi officials said the photos included unidentified people who died at the Hajj – not just in the stampede.
Spokesman Maj Gen Mansour al-Turki told the Associated Press that some were foreign nationals who lived in Saudi Arabia and carried out the Hajj without the required permits.
Others were among the 109 people who were killed when a crane collapsed at the Grand Mosque in Mecca on 11 September, he said.
Confusion about how many people died in last week’s stampede mounted after Indian Foreign Minister Sushma Swaraj tweeted on Sunday that the Saudi authorities had released photos of 1,090 pilgrims who died.
Pakistani and Indonesian officials also indicated that they have been sent more than 1,000 such images.
On Tuesday, a Nigerian Hajj official from Kano, Abba Yakubu, told the BBC’s Yusuf Ibrahim Yakasai that he had been to Jeddah, where the dead from the stampede were being processed.
Mr Yakubu said that in total, 14 lorries loaded with bodies were brought to the city.
He added that so far 1,075 bodies had been offloaded from 10 lorries and taken into the morgues. Four lorries had yet to be dealt with, Mr Yakubu said.
Several countries have been severely critical of the way the Saudi authorities have handled the accident’s aftermath, notably Saudi Arabia’s regional rival Iran, which lost at least 228 people in the disaster.
The stampede was the deadliest incident to hit the Hajj in 25 years.
The crush occurred as two large groups of pilgrims converged at right angles as they took part in the Hajj’s last major rite – stone-throwing at pillars called Jamarat, where Satan is believed to have tempted the Prophet Abraham.
As well as the fatalities, 934 people were injured.
Saudi Arabia’s most senior cleric, Grand Mufti Sheikh Abdul Aziz bin-Abdullah al-Sheikh, has defended the authorities, saying the stampede was “beyond human control”.
King Salman has ordered a safety review into the disaster.