The bid to remove her from the leading post at the election watchdog was supported by 58 of Lithuania’s 141 lawmakers, while 65 were against and three abstained.
The decision to remove her required at least 71 votes in support.
The no-confidence procedure was initiated by the parliament’s opposition groups, which accused her of the commission’s “chaotic performance” and for taking decisions on her own.
Matjošaitytė rejected the criticism of procrastinating matters involving the ruling Lithuanian Farmers and Greens Union, pledging to be impartial in her future work.