Moreno did not specify what part of the transportation network was being targeted.
He said the alleged suicide bombers, Mohamed Shoaib, Mehmooh Khalib and Imran Cheema, arrived in Barcelona between October and mid-January.
He identified the ideologues as Maroof Ahmed Mirza, described as a key religious leader and organiser of the cell, and Mohammad Ayud Elahi Bibi.
Spanish authorities arrested 12 Pakistanis and two Indians on Saturday but later released two of them.
Bomb-making materials and timers were seized in raids on five homes over the weekend, the government had said, adding that the attack was in an advanced stage of preparation.
Madrid's commuter rail network was bombed in March 2004, killing 191 people and leaving more than 1,800 injured.
Late last year the national court convicted 21 suspects tried for terrorism and other charges connected with the bombings.
Also in late 2004, Madrid police arrested more than two dozen suspects who were allegedly planning a massive bomb attack against the national court with an explosives-laden truck.