The duo have been strongly linked with moves away from San Mames this summer, and the trainer has excluded them from the squad until they sort out their futures.
However, the Argentine tactician rejected talk of a rift between him and the two players, and insisted he is not the reason why they want to leave the club.
"Athletic is going through a difficult time and it is not helped by malicious information," the coach told Marca.
"I asked Llorente and Martinez if I was the reason why they do not not want to stay at the club, and the both said 'no'.
"Had they answered ‘yes’, then I would have acted accordingly."
The coach then went on to reject claims that another Bilbao player, Fernando Amorebieta, is also out of team training because of an ongoing contract dispute.
"I deny that Amorebieta is not training with the group as a result of negotiations with the club. The club would need my intervention to make such a scenario so.
"It is unfair what is being reported and I deny it. In addition, Toquero and Susaeta are in the same situation as Amorebieta, which rules out the scenario."