Paul Kagame (R) led the forces that stopped the killings in 1994
Rwanda has urged foreign governments and Interpol to ignore Spanish arrest warrants for 40 Rwandan army officers on genocide charges.
The Rwandan foreign ministry called the warrants "bogus" and "ridiculous", and said the case was based on falsehoods, racist language and genocide denial.
Spain's high court has accused the officers of involvement in mass killings in the early 1990s.
Spanish courts can prosecute war crimes even if the offences took place abroad.
Judge Fernando Andreu also indicted the Rwandan officers for the murder of nine Spanish citizens, including six missionaries.
He said he had evidence implicating Rwanda's current President Paul Kagame, who has immunity from prosecution.
But Rwanda's foreign ministry said the judge had never visited Rwanda or the Democratic Republic of Congo, where some of the killings are alleged to have taken place.
"He just sat in Madrid, listened to well-known detractors of Rwanda and based on their falsehoods, which he never tried to cross-check, just went ahead and issued indictments," a statement says.
It adds that he has not tried to liaise with Rwanda's judicial authorities to seek the officers' arrest.
Judge Andreu began considering the case in response to a complaint from a human rights group in 2005.
During a 100-day period in 1994, an estimated 800,000 Rwandans were killed, mainly ethnic Tutsis at the hands of radical Hutus.
The genocide came to an end when Tutsi-led rebels under Paul Kagame took control.
But the judge said that, after taking power, the army under Mr Kagame carried out mass killings of Hutus in Rwanda and in refugee camps in what was then neighbouring Zaire.
The indicted members of the military are also accused of crimes against humanity, genocide and terrorism.
In 2006, French judge Jean-Louis Bruguiere issued indictments against nine close aides of Mr Kagame, sparking a huge diplomatic row.
Previous attempts by Spanish judges to open human rights cases against foreign figures have largely failed.
In 1998, former Chilean president Augusto Pinochet was indicted while in London but not extradited.