Critics charged President Mohammed Morsi with exceeding his mandate.
Abdel-Maguid Mahmoud was quoted by Egypt's official news agency as saying that he will remain in his post. His brief statement came just hours after Morsi ordered him to leave his position as prosecutor general and become the ambassador to the Vatican.
In a comment to a news website, The Seventh Day, Mahmoud said, "I am upset" over Morsi's order.
Egyptian law protects the prosecutor general from being ousted by the president, A judges' club called for an emergency meeting to protest Morsi's decree which they see as a blow to the judiciary.
Ahmed el-Zind, the head of the powerful association of judges, said that the judges will not bow to Morsi's decision.
"This is a farce ... we will not bow," he said and added, "the era of tyrants is over."
"O people of Egypt are you willing to topple down judiciary?" said el-Zind, an opponent to Morsi and his group The Muslim Brotherhood. "We announce from here our solidarity with the prosecutor general," he added.
It was not possible to reach presidency spokesmen to comment on Mahmoud's refusal to step down. Unconfirmed reports suggested that the country's Minister of Justice Ahmed Mecci has submitted his resignation.
Though Morsi's decision had considerable public support, it appeared similar to his move to restore the Islamist-dominated parliament to session despite a decree by the Supreme Constitutional Court, which dissolved it over election law violations. The parliament then met in a single, short session.
Morsi has been sending mixed messages to public. He has been shaking up the country's state institutions removing much hated figures from Mubarak's regime, but by replacing them with Islamists or sympathizers, he has sparked concerns from many liberal and secular parties.
The latest dispute over removing the prosecutor general carried a double message.
Morsi's goal appeared to be to appease public anger over the acquittal on Wednesday to 24 loyalists of Mubarak over their role in last year's attack on demonstrators, known as the "Camel Battle."
Many accused Mahmoud as failing, either intentionally or due to incompetence, to present a strong case against the accused, leading to their acquittal.
The defendants were found innocent on charges of manslaughter and attempted murder. Judge Mustafa Abdullah on Wednesday said the defendants were acquitted because witness testimony was weak and "driven by grudges between witnesses and the defendants due to partisan differences."
The "Camel Battle" took place Feb. 2, 2011, when men riding horses and camels charged into crowds on Cairo's Tahrir Square, setting off two days of clashes that ended with killing of nearly a dozen of people, a turning point in the 18-day popular revolution that ended with Mubarak's ouster.
Nearly 1,000 protesters were killed in the uprising against Mubarak, most during clashes with security forces in the early days of the uprising, which began on Jan. 25, 2011. But almost none of the officials and policemen brought to trial for the deaths have been found guilty. Most were released for lack of evidence and poor investigation.
That prompted criticism from a public weary from months of turmoil and concerned that members of Mubarak's regime wound not be held accountable for the deaths of protesters. As a Mubarak-era official who prepared politicized cases against regime opponents, Mahmoud's removal has been a top demand of protesters.
On the other hand, the timing of Morsi's move was seen as an attempt to defuse the anger of liberals and secular activists, his rivals, who were preparing for Friday rallies against Islamist rule called "the Friday of Accountability," as well as demanding reform of a key assembly assigned to write the country's new constitution. The body is monopolized by Islamists and has produced proposed provisions seen as suppressing civil liberties.
When asked whether the dismissal is linked to the court acquittals, Morsi's chief of staff, Ahmed Abdel-Atti, also a member of the Brotherhood, said, "the general political atmosphere affects decisions by the state and the president."
The acquittals were condemned by Morsi's Muslim Brotherhood, which said it would join Friday's protests to demand retrials. When news spread about Morsi's removing Mahmoud, Brotherhood protesters gathering in Tahrir Square chanted, "we love you Morsi," and beating drums.
Abdel-Atti said Morsi has met with top advisers and ministers and urged a new fact-finding mission to speed up work to put in place a new law to "protect the revolution" and allow new trials for former regime members, top security officials and police accused in the killing of protesters during the uprising.
Human rights lawyer Ahmed Ragheb said that it will take more than removing the prosecutor general to reform the judiciary.
"The judiciary is packed by judges who acted as Mubarak's soldiers. Changing the prosecutor general won't change that. Instead, drastic reforms are needed," he said.