The political bureau of the GNC, headed by former president Ali Abdullah Saleh, had announced Hadi's sacking on Saturday.
Hadi was accused of soliciting UN sanctions against Saleh, his predecessor who stepped down in 2012 after an almost year-long uprising.
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The Security Council slapped sanctions on Saleh and two allied Shiite rebel commanders for allegedly threatening the UN-backed political transition in the impoverished country.
Some 200 GNC members from southern provinces at Thursday's meeting in Aden said the dismissal of Hadi, a native of the south, and his political advisor, Abdelkarim al-Ariani, was invalid because it did not comply with the party's internal regulations.
They called on the political bureau to reconsider its decision and to apologise to both Hadi and Ariani, the GNC's second vice president, who it said remained "legitimate leaders" of the party.