The 25-year-old returned to England after Ghana shared the spoils 1-1 with Egypt in the final game of the 2018 Fifa World Cup qualifiers. Although, he missed the game, he was not part of the Magpies' matchday squad that suffered a 4-1 defeat at Old Trafford on Saturday, with reports claiming he could be out of action for at least two weeks.
"I want to be very, very honest and clear. He had a kick during the game against Bournemouth and after, when he shot he was feeling it a little bit," Benitez told Gazette.
"He put some ice on it and said he was fine. Then he went away with the national team. He had a training session and they sent him back.
"It's not the case that they were using him and then something happened. He had a little problem and then he went there, couldn't play and he came back. It's not that it's their fault. It's just something that happened," he added.
In Atsu's absence, Benitez will have to manage with Ayoze Perez, Rolando Aarons or Jacob Murphy as they fight to push up on the log.
"Hopefully, we can manage with Rolando or Jacob if we need to do it, or maybe with the movements of Ayoze," the Spanish gaffer said.
"It's what we have and we have to adapt to deal with what we have and see if we can do it."
Atsu boasts of 11 league appearances so far, including 10 starts and has scored one goal.