(Updates with attorney general comment)
By Mike McDonald
GUATEMALA CITY, April 19 (Reuters) - The genocide trial of former Guatemalan dictator Efrain Rios Montt was mired in uncertainty on Friday as judges squabbled over who should hear the case following an order to annul nearly 18 months of proceedings.
The trial was suspended on Thursday when Judge Patricia Flores, who was originally assigned to the case, ruled all actions taken since she was recused in November 2011 were void, citing an order from the country's top courts.
On Friday, Guatemala's attorney general said the ruling was illegal, echoing the view of one of the presiding judges who asked the constitutional court to resolve the matter.
Rios Montt, 86, is charged with genocide and crimes against humanity for a counterinsurgency plan conceived under his 1982-1983 rule that killed 1,771 members of the Ixil indigenous group in one of the bloodiest phases of Guatemala's civil war.
His trial was hailed as a landmark in efforts to bring justice for victims of the 1960-1996 civil war. It took years to set in motion after Rios Montt's lawyers repeatedly delayed efforts to make the retired general stand trial.
Attorney General Claudia Paz y Paz said the government had lodged an appeal against Flores' decision.
"I have never seen a case where something like this has happened," Paz y Paz told Reuters. "It is illegal."
"What worries me is the image of the justice system in the eyes of the people," she said, adding she was concerned that the constitutional court had no deadline to resolve the matter.
Flores' announcement sparked anger among victims of the civil war, which claimed the lives of about 200,000 people and caused the disappearance of another 45,000.
Judge Yasmin Barrios, who has overseen Rios Montt's trial with two other judges since it began last month, said Flores' order was against the law. She suspended the hearings on Friday pending a ruling by the Constitutional Court to settle the dispute.
"No public official or citizen is obliged to execute illegal orders ... and this court will not do it," Barrios told the court in Guatemala City where Rios Montt has been on trial.
More than 100 people applauded Barrios' decision and began to chant "justice, justice" as she left the courtroom.
Flores' intervention came days before prosecutors had hoped for a judgment in the trial, which has stirred up powerful emotions in Guatemala and cast a harsh light on the actions of the armed forces during the civil war.
More than a hundred victims have testified during the trial, retelling stories of torture, rape and arson that they endured during Rios Montt's 17-month rule.
One prosecution witness even implicated President Otto Perez, himself a retired general, saying soldiers under his command carried out atrocities in the war.
Manuel Baldizon, head of the opposition Renewed Democratic Liberty Party (Lider) and runner-up in the 2011 presidential election, accused Perez and his conservative Patriot Party of pressuring the Guatemalan courts to shut down the trial.
Baldizon told Reuters that the government was trying to cover up evidence linking Perez to war crimes and pledged to investigate his political adversary if he ever became president.
"They have created an incredible new level of opacity across the board, including the justice system," he said.
The United Nations' human rights office voiced alarm on Friday at the suspension of the trial, calling it a blow to victims who have waited decades for justice.
Rights groups in Guatemala also expressed dismay.
"(Flores') decision is unimaginable," said Francisco Dall'Anese, a prosecutor who heads the U.N.-backed Commission Against Impunity in Guatemala.
"Guatemala's judicial code is very clear in stating that the process cannot be rewound to a previous phase that has already concluded in order to correct errors," he added.
Initially involved in the case, Flores was recused after a lawyer representing another man then under investigation with Rios Montt complained she would not be impartial.
She was not informed of the recusal until 2012, when she stepped down. Prosecuting lawyers appealed that decision and a court overturned her recusal last month. Defense lawyers then argued she should have been kept on the case. (Writing by Dave Graham; Editing by Simon Gardner and Stacey Joyce)