Citing Algerian security sources, Anis Rahmani of the private television channel Ennahar told AFP the army discovered "the bodies of 25 hostages" as they sought to secure the sprawling Sahara site at In Amenas.
"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 that began Wednesday.
In Tokyo, a foreign ministry official said: "We are in a position not to comment on this kind of information at all. Please understand."
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.
Governments scrambled to track down missing citizens as details emerged of the deadly showdown after Islamists of the "Signatories in Blood" group raided the plant on Wednesday, demanding an end to French military intervention in Mali.
British Prime Minister David Cameron said in a statement that "it is now clear that this appalling terrorist incident in Algeria is now over.
"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."
Japanese engineering firm JGC Corp had said 10 of its Japanese and seven of its foreign workers remained unaccounted for, before the reports became known of Japanese hostages being executed.
Kuala Lumpur said JGC had told it one of two Malaysians still unaccounted for is dead whilst the fate of the other was unknown.
Norway's Statoil, which operates the gas plant alongside Britain's BP and Sonatrach of Algeria, said the situation remains "unresolved" for five Statoil 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," Algeria's 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.
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.".
Forced to wear explosives, he fled when the hostage-takers' convoy he was in came under fire on Thursday.
In Saturday's final assault, "the Algerian army took out 11 terrorists, and the terrorist group killed seven foreign hostages," state television said, without giving a breakdown.
A security official told AFP it was believed the foreigners were executed "in retaliation."
The militants, whose leader is Algerian Mokhtar Belmokhtar, a former Al-Qaeda commander, first killed a Briton and an Algerian on a bus on Wednesday before taking hundreds of workers hostage when they overran the In Amenas plant.
Most of the 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 in a statement.
At least one American had already been confirmed dead before Saturday's final assault.
Cameron on Sunday refused to criticise Algeria, saying the attack on the In Amenas gas complex 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 told AFP the hostage-takers spoke in different Arabic dialects.
"From their accents I understood one was Egyptian, one Tunisian, another Algerian and one was speaking English or (another) foreign language," he said after escaping on Thursday.
"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 was needed "to defeat terrorism" in the West African country and its neighbours.
Malian and French troops patrolled the outskirts of the contested northern town of Diabaly 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 Sunday that the hostage-taking in Algeria showed the need to be "relentless in the face of terrorism."