Vainiutė informed Prime Minister Saulius Skvernelis about her decision to resign during their meeting on Tuesday morning, the government's press office said.
"I understand and respect the minister's decision in this situation", Skvernelis said in a press release after the meeting.
"I am grateful to her for her work and for launching significant reforms that nobody had undertaken for years although they had been aware of the deep-seated problems in the Centre of Registers, in the prison system and in other areas", he said.
Rasa Kazėnienė, an auditor with the Justice Ministry, said at a news conference last week that Deputy Justice Minister Raimondas Bakšys had blocked an initiative by her and her colleague to turn to law-enforcement bodies over the material collected during an audit of the Pravieniškės correctional facility.
According to the auditor, Vainiutė was also present at the meeting.
Bakšys says that he just wanted to wait for the audit to be completed so that the investigations did not intervene with the processes.
The deputy minister categorically dismissed the allegations, but he handed his resignation on Monday, saying that he could not continue under the circumstances.
President Grybauskaitė said on Monday that the justice minister was not coping with her duties.
Ministers in Lithuania are appointed and dismissed by the president on the prime minister's recommendation.
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