The Spanish daily El Pais reported Sunday that Rajoy is being confronted with differing takes on the separatist group ETA from the National Intelligence Center, the Guardia Civil and National Police, each of whom have sharply convergent opinions on whether the separatists continue to pose an imminent threat.
The ETA, blamed for more than 820 deaths in its 50-year fight for independence an area that is in both Spain and France, announced in 2011 it had renounced violence, formally declaring a "definitive cessation of its armed activity."
Since then, many of its leaders have been arrested and caches of arms seized.
But the group has refused to disband or voluntarily turn over its weapons unless its members are released from prison. The ETA proposed talks with the government in November but Madrid rejected the offer and demanded the ETA dissolve as a precondition.
El Pais reported the intelligence service, known by the Spanish acronym CNI, contends that based on foreign intelligence and information from infiltrators, the ETA is essentially dead and isn't capable of further violent action.
The Guardia Civil, which has an intelligence unit in France, indicates ETA is very weak but doesn't rule out a possible terrorist strike. It reportedly has told Rajoy that youth factions within the group are very radical and are in disagreement with older members over the stated goal to a forge new path away from violence.
Spain's National Police, meanwhile, came in at the other end of the spectrum, saying in a report supported by Europol that the band "maintains its logistic structure and continues its role as a clandestine organization."
The police said there is a clear concern ETA could resume violent action, especially after the government rejected talks without an announcement ETA was disbanding.
ETA issued a toughly worded statement in March in which it criticized the government for its "negative and obstructive" attitude toward possible talks. The message came after the Norwegian government expelled three of its members due to the lack of progress in the peace process.
While the Spanish Interior Ministry said it's played no part in the expulsions, police sources told El Pais said the decision had the backing of the Spanish administration.
The newspaper reported Rajoy was "taken aback" by the differing assessments, which came only days after a secret April 10 meeting with Basque President Inigo Urkullu, to whom he delivered a prisoner re-entry plan.
The assessments of ETA's threat were so opposite and contradictory, Rajoy and Interior Minister Jorge Fernandez reportedly decided to try to iron out the differences in meetings at Moncloa Palace.
The prime minister summoned the heads of the three bodies separately and demanded they reveal data or sources they used to reach their very different conclusions.
In the meetings, El Pais said, the Civil Guard touted the experience of its field units, the CNI cited spies abroad, international contacts and infiltrators while the police voiced "total distrust" of the others' evidence.