Citing security sources, Anis Rahmani of private television channel Ennahar said the army discovered "the bodies of 25 hostages" as they secured the sprawling In Amenas Sahara site.
Algerian Communications Minister Mohamed Said had earlier told a radio station: "I fear that it (the toll) may be revised upward," after at least 23 foreigners and Algerians, mostly hostages, were killed over the four days.
It was not immediately clear if the 23 were included in Sunday's 25 toll.
"In all nine Japanese were killed," one Algerian witness identified as Brahim said a day after special forces swooped on the gas plant run by Britain's BP, Norway's Statoil and Sonatrach of Algeria to end the siege.
The first three were killed as they tried to escape from a bus taking them to the airport as the militant attack unfolded, they said.
"We were all afraid when we heard bursts of gunfire at 5:30 am (0430 GMT) on Wednesday, after we realised that they had just killed our Japanese colleagues who tried to flee from the bus, and whom they had taken to another site," said Riad, who worked for the Japanese engineering firm JGC Corp.
The gunmen then took the others to the residential compound, where they had seized hundreds of hostages, he said.
"A terrorist shouted 'open the door!' with a strong north American accent, and opened fire. Two other Japanese died then and we found four other Japanese bodies" in the compound, he added, choking with emotion.
In Tokyo, a foreign ministry official said: "We are in a position not to comment on this kind of information at all. Please understand."
The harrowing witness accounts came after Japanese Prime Minister Shinzo Abe said he had received "severe information" by phone from Algerian Prime Minister Abdelmalek Sellal about the end of the stand-off.
Governments scrambled to track down their missing citizens as more details emerged of the deadly showdown after Islamists of the "Signatories in Blood" group raided the plant, demanding an end to French military intervention in Mali.
"Tragically, we now know that three British nationals have been killed, and a further three are believed to be dead. And also a further British resident is also believed to be dead," British Prime Minister David Cameron said.
Norway's Statoil said the situation remains "unresolved" for five of its employees.
"We will, and we must, keep hoping for more positive news from Algeria. However, we must be prepared to deal with bad news in the next few days," Statoil CEO Helge Lund said.
Thirty-two kidnappers were also killed in the 72-hour stand-off, and the army freed "685 Algerian workers and 107 foreigners," the interior ministry said on Saturday.
Relatives of Kenneth Whiteside, 59, from Glenrothes in Scotland, were "devastated" after hearing that an Algerian co-worker claimed to have seen him being shot but dying bravely with a smile, Britain's Mail on Sunday reported.
And the mother of survivor Stephen McFaul, 36, from Belfast, told the Sunday Mirror her son will "have nightmares for the rest of his life after the things he saw."
A security official told AFP it was believed seven foreigners were executed "in retaliation" on Saturday during the final assault that state television said also killed 11 militants.
The gunmen, whose leader is Algerian Mokhtar Belmokhtar, a former Al-Qaeda commander, first killed a Briton and an Algerian on a bus before taking hundreds hostage at the plant.
Most hostages were freed on Thursday when Algerian forces launched a first rescue operation which was widely condemned as hasty.
But US President Barack Obama and his French counterpart Francois Hollande said responsibility for the deaths lay with the "terrorists."
"The blame for this tragedy rests with the terrorists who carried it out, and the United States condemns their actions in the strongest possible terms," Obama said after at least one American had already been confirmed dead.
Cameron on Sunday refused to criticise Algeria, saying the attack had been an "extremely difficult" situation to deal with.
Hollande called Algiers' response "the most appropriate" given it was dealing with "coldly determined terrorists ready to kill their hostages."
Monitoring group IntelCenter said the hostage-taking was the largest since the 2008 Mumbai attack, and the biggest by jihadists since hundreds were killed in a Moscow theatre in 2002 and at a school in the Russian town of Beslan in 2004.
Algerian driver Iba El Haza, who had escaped on Thursday, said the hostage-takers spoke in different Arabic dialects.
"The terrorists said: 'You have nothing to do with this, you are Algerians and Muslims. We won't keep you, we only want the foreigners'."
Hollande said French troops would stay in neighbouring Mali as long as necessary "to defeat terrorism."
Malian and French troops patrolled the outskirts of the contested northern town of Diabaly on Sunday in a show of muscle a day after West African leaders demanded speedy UN aid to rout Islamists holding the vast desert north.
French Foreign Minister Laurent Fabius told Europe 1 radio that the hostage-taking in Algeria showed the need to be "relentless in the face of terrorism."