Santos said in a national presentation the plan would make the country's rail infrastructure more modern and environmentally sustainable, and allow for train travel from Lisbon and Porto to Madrid in about three hours.
The plan includes high speed trains in the 10 largest Portuguese cities and rail links in all districts.
It would halve the travel time between Lisbon and Porto from the current 2 hours 50 minutes. A third crossing over the Tagus will shorten the trip to Lisbon from southern regions by at least 30 minutes, said Federico Francisco, coordinator of the working group drafting the plan.
Portugal sees train travel as a way to reduce driving and meet its objective to become carbon neutral by 2045.
It aims to boost rail travel's share of total passengers to 20% from 4.6% and rail transport of goods to 40% from 13%.