Mr Echeverria, now 80-years-old, was asked about two massacres - one in 1968 when he was interior minister and also the so-called Corpus Christi massacre in 1971 when he was president.
The massacres formed part of Mexico's so-called dirty war when thousands of left-wing activists and radicals were killed and hundreds more went missing.
It is thought to be the first time a Mexican leader has been ordered to appear before a prosecutor.
Criminal acts
Mr Echeverria's court appearance comes as part of an investigation into alleged human rights abuses ordered by the current Mexican President, Vincente Fox.
His National Action Party came to power in 2000, defeating the Institutional Revolutionary Party, or PRI, which had ruled Mexico for more than 70 years.
Mr Fox took action after the head of Mexico's Human Rights Commission handed him a sealed envelope containing the names of current and former officials implicated in criminal acts of political repression.
The names were not made public, but a special prosecutor was appointed in January to investigate the allegations.
Human rights advocates claim Mr Echeverria, along with his successor, Jose Lopez Portillo, masterminded the disappearances of anti-government protesters and guerrillas.
In the case of the Corpus Christi massacre, Mr Echeverria is alleged to have received reports from the field as thugs beat and shot students protesting against his regime, the Associated Press news agency reported.
Protesters' hope
Both Mr Echeverria and Mr Portillo have denied any involvement in the disappearances.
However, Mr Fox is keen to follow up on his election promise to root out corruption and punish those responsible for human rights abuses.
BBC correspondents say the work of the special prosecutor is being seen as a test of the president's determination.
Several demonstrators stood outside the courtroom, with one carrying a sign stating "Your time has come".
"There has never been a presidential term in which there were so many deaths as in his (Mr Echeverria's) term," demonstrator and writer Leopoldo Ayala, a student who was present at the 1968 massacre, told the Associated Press news agency.
"You cannot have democracy without clearing up the murders."