Mikėnaitė tendered her resignation to Justice Minister Milda Vainiutė on Monday morning, the Justice Ministry said.
The minister accepted the director's resignation.
Mikenaite said several weeks ago that she had appealed Vainiute's decision to suspend her from duties to court.
The Justice Ministry is conducting a probe into possible official misconduct by Mikėnaitė and Edvardas Kviatkauskas, head of the Kaunas Remand Prison, related to the use of public funds and public procurement. The justice minister in early February suspended both officials from their duties.