Diokno arrived in Malacañan Palace around 1pm and tendered his resignation at around quarter to 2 p.m., ABS-CBN sources said.
Aquino said he has accepted Diokno's resignation.
Asked about the resignation, Justice Secretary Leila de Lima said: "Diokno's resignation [is] the most honorable, selfless way to go."
Diokno was in hot water for the escape of New Bilibid Prisons (NBP) inmate Antonio Leviste last May 18, reportedly not the first of the former Batangas governor's several unauthorized trips outside the facility.
Leviste's arrest outside a Makati City building that he owns led to an investigation of the supposed VIP treatment of high-profile inmates in NBP.
Diokno's resignation came ahead of Aquino's action on a Department of Justice(DOJ) fact-finding committee report submitted to Malacanan today.
The contents of the 36-page report, as well as Justice Secretary Leila de Lima's 8-page memorandum, have yet to be divulged to the public.
Diokno earlier said he is not to blame for the former Batangas governor's slipping in and out of jail and eventual arrest outside the NBP compound. He said he supervises operations of the NBP as well as 6 other penal colonies nationwide.
"Paniwala ko po di ako dapat sisihin dito. Ako (po) sa policy-making sa opisina. Sad to say, ang opisina (of the BuCor Director) nandoon lang sa NBP," he told a justice department fact-finding panel.
Asked who should take the blame, he said: "The Chief Superintendent...the superintendents of the minimum (security compound), BRSS (Bureau Reservation and Support Services)...Lahat yan dapat maimbestigahan mabuti."
Diokno admitted that he received raw information about Leviste's unauthorized trips outside the prison, but did not cancel his "sleeping-out" privilege despite the information.
Instead, he sent several memos to prison superintendents to report all movements of high-profile inmates inside NBP.
"May raw info na ako na pumupuslit si Leviste. I did a memo to all of superintendents to monitor nila. I am not obligated to guard them. I am in charge of policy-making. I told them that if they didn't implement, they would be charged administratively," he said.
Diokno said he also called for a command conference of the "council of elders," composed of leaders of each brigade, to warn them against leaving the prison without authorization. He said Leviste is a member of the council of elders.
"Sabi ko, 'Governor, itigil niyo na yung paglabas diyan dahil kung kayo ay lumalabas diyan, sa aking administrasyon ay hindi pwede sapagkat dito sa akin ipahuhuli ko kayo at icha-charge ko kayo,'" he recalled telling Leviste.
Asked why he did not cancel Leviste's sleep-out status that allowed him to stay in a reservation outside the minimum security jail, Diokno said: "Yung iba sa kanila pwede hong gawin yan pero sa akin hindi ko pa nakikita. Raw information lang ang dumadating sa akin. Hindi naman niya sinasabing totoo. Wala naman akong kasalanan dahil ang approach natin diyan ay reformation."
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