Speaking ahead of a planned visit by Etihad boss James Hogan to Rome on Tuesday, Gabriele del Torchio said in a statement that layoffs were "painful but necessary to restore development and a future to the entire sector".
At talks between Alitalia and unions over the weekend, there was a partial agreement on laying off 1,635 workers - with some being moved to other companies in the aviation sector and others receiving redundancy packages.
Most unions have agreed, with the exception of Italy's biggest union, the CGIL, and the far-left USB union.
The agreement "has been signed by unions representing more than 70 percent of Alitalia workers", Transport Minister Maurizio Lupi, who has been mediating the management-union negotiations, was quoted by the ANSA news agency as saying.
Etihad Airways is planning to buy a 49 percent stake in debt-laden Alitalia, which currently employs 12,800 people.
Etihad's initial investment is expected to be around €560 million euros ($762 million), and €660 million more has been mooted in future to develop the airline.
Del Torchio said the agreement on layoffs "is another decisive step on a road map that I hope will soon allow us to define our strategic alliance with Etihad Airways".
"Etihad's entry into Alitalia capital will create a new and very competitive sector of the Italian economy, strongly oriented towards foreign markets," Del Torchio said.