Almost 90 percent of its 12,500 employees had participated in a vote and more than half those taking part opposed the deal, with more than a third of ballots still to be counted.
They opposed a plan for 1,700 job losses and a 8 percent salary cut, despite the government saying over the weekend that there would be no alternative. The company's coffers are empty.
Italian press reports said Alitalia directors may as soon as Tuesday -- a public holiday in Italy -- ask the state to establish a "special administration" for a possible takeover or liquidation.
The company is de facto controlled by Etihad Airways, which acquired a 49 percent stake when it saved Alitalia from bankruptcy in 2014.
The pressure to find a solution has been intense, with Alitalia's liquidity expected to run out this month without emergency funding, leaving its fleet grounded.
Etihad and the Italian banks Intesa Sanpaolo (Amsterdam: IO6.AS - news) and UniCredit (EUREX: DE000A163206.EX - news) have said they would only inject new funds if the unions agree to the new collective labour agreement and cuts.
The Italian government, which acted as a mediator in negotiations, warned on April 18 that a "no" victory would not only be costly but potentially fatal for the company.
Alitalia has been hit hard by competition from low-cost companies and has been accumulating losses for years.