Basque media reported the denial on Friday, citing a message received from the armed group.
Spanish authorities at first blamed ETA outright for the attacks and have since called the outlawed group the prime suspect while not ruling out Islamist groups.
"An ETA message has arrived saying that it bore no responsibility for the attack," a presenter for ETB Basque public television said.
The Basque newspaper Gara also said on its website it had received a phone call from a person claiming to represent ETA saying it "had no responsibility whatsoever" for the attacks which involved 10 bombs set off simultaneously on four trains on Thursday morning.
There was no way to independently confirm the authenticity of the call, but ETA has claimed responsibility for past attacks through ETB and Gara.
Across Spain police estimated more than eight million people took to the streets on Friday in an unprecedented show of grief and fury at Thursday's train attacks.
The demonstrations - vast seas of umbrellas in rain-soaked cities and towns - were by far the biggest the country has ever seen, easily beating the previous record set in February last year when the population protested against its government's support of the US war on Iraq.
In Madrid alone two million people took to the streets, the website of El Mundo newspaper said.
As three days of mourning got underway, Spain observed a minute's silence and flags flew at half-mast in memory of the 199 people killed in the Madrid train bombings.
Prime Minister Jose Maria Aznar vowed on Friday to "leave no stone unturned" to find those responsible for the country's worst attack.
Spanish media and authorities described the attacks as "our own September 11", but were divided as to who was to blame.
In a media conference after an emergency cabinet meeting, Aznar refused to pin blame on any one group, saying only "all the forces of democracy and society must stand up" against terrorism.
Focus on ETA
Officials in the government of the Spanish leader, who escaped an ETA attempt on his life in 1995, continued to focus suspicions on the Basque group.
"Everything appears to indicate that this terrible carnage is the work of ETA"
Spanish Foreign Minister
"Everything appears to indicate that this terrible carnage is the work of ETA," Foreign Minister Ana Palacio told French radio Europe 1. "We have very strong clues, very strong precedents."
But she added Spain could not completely rule out the possibility that al-Qaida was behind the attack. The London-based Arabic newspaper Al-Quds Al-Arabi reported that it had received a claim of responsibility from the group.
A stolen van was discovered on Thursday containing seven detonators and a tape with Quranic verses in Arabic 35km from Madrid.
The moderate leader of the autonomous Basque region, Juan Jose Ibarretxe, said there existed "reasonable doubt" as to the perpetrators.
PM's tough stance
But Aznar's ultra-hard line on Basque radicalism, which he sees as threatening Spanish unity, has won him bitter enmity among Basque nationalists and the leader of the banned radical party Batasuna on Friday accused him of lying by blaming ETA, with which the group has links.
At least 198 people were killed
and more than 1400 injured
Aznar himself narrowly escaped assassination in a 1995 car-bomb attack linked to ETA.
The leader of Batasuna, Arnaldo Otegi, said of Aznar: "He is lying and he knows who did it... He wants to maintain this hypothesis until after Sunday's election."
The bombings occurred in four suburban trains and three railway stations in south-east Madrid during the morning rush-hour on Thursday.
Ten bombs went off within minutes of each other, sowing carnage and sending shockwaves around the world. It was Europe's worst attack since the 1988 Lockerbie bombing that killed 270 people.
US support for Spain
A total 377 people remained in hospital on Friday morning, 45 of them in a critical state and 15 listed as being in very serious condition, according to the latest toll.
The US has come out loudly in support of Spain following the attacks.
"I appreciate so very much the Spanish government's fight against terror, their resolute stand against terrorist organisations like the ETA," US President George Bush said on Thursday.
US homeland security chief Tom Ridge said during a trip on Friday to Thailand: "The savagery, the inhumanity of those attacks undoubtedly will do nothing but strengthen an international resolve to combat terrorism in whatever form it takes and in whatever faction is responsible for it."
Aznar said 14 foreigners - most of them Latin Americans living in Spain - were among the dead, and he pledged to give Spanish citizenship to families caught up in the tragedy.