The vote is seen as a major blow to UN efforts to unify the country`s two rival parliaments.
Islamic State militants have stepped up attacks in recent weeks, targeting the country`s oil infrastructure.
Libya has been in chaos since the 2011 overthrow of Colonel Muammar Gaddafi.
Of 104 members attending the session in the eastern city of Tobruk, 89 voted against backing the government, Reuters news agency reports.
The Tunis-based Presidential Council now has 10 days to put forward a new, shorter list of ministers, Reuters adds.
Libya`s state oil company said earlier that the country had lost $68bn (£48bn) in potential oil revenues since 2013, in comments reported by the UK`s Financial Times newspaper.
Western nations hope the formation of the new government will help bring stability and tackle the growing threat of the so-called Islamic State group (IS).
IS militants have taken advantage of the political vacuum to expand their presence in the country.
Libya conflict: UN-backed unity government rejected
26 January 2016
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Libya`s internationally recognised parliament has rejected a unity government named last week under a UN-brokered deal aimed at uniting the country`s warring factions.
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