The 21-year-old scored in the 1-0 win over basement side Crystal Palace in Newcastle's last home game but Benitez said his compatriot faces a spell on the sidelines after aggravating the injury.
"Merino will be out for at least a couple of weeks. We will see how he is doing," Benitez told a news conference on Friday, before adding Merino would miss Spain's Under-21 2019 European Championship qualifiers against Iceland and Slovakia this month.
"He will not go away with the national team and he will not be available for this game. We will have to wait and see how his lower back is.
"He was feeling the pain the other day. We know he is not available so we have to concentrate on the other players, and I think it is fine."
Benitez said he had at least four options to replace Merino and could also play Congo defender Chancel Mbemba as a makeshift midfielder against Eddie Howe's 19th-placed side.
"We have four or five midfielders. We have (Mohamed) Diame, (Henri) Saivet, (Isaac) Hayden and (Jonjo) Shelvey, and if we need... we can bring Mbemba in as a midfielder – he played there in the Africa Cup of Nations. I think we have enough bodies."
Newcastle, who have 14 points from 10 games and sit ninth in the table, have not been beaten in nine of their last 10 league games at St James' Park.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Toby Davis)
