In his second season in Spain since joining from Bayern Munich, Kroos was an unused substitute in Real's last two outings, with Benitez preferring Brazil international Casemiro in the centre.
Kroos made 12 assists and netted two goals in 55 appearances in 2014-15 but his influence has waned this term and he has set up only one goal and scored none in 18 outings.
The 25-year-old watched from the bench as Real slipped to a 1-0 defeat at Villarreal in La Liga last weekend and will be hoping to win his place back for Sunday's game at home to Rayo Vallecano.
"Toni Kroos is a great player and when I have spoken to him he has always indicated he is available to play wherever we think is best," Benitez told a news conference. "He remains a fundamental player for us."
Real are third in the standings after 15 games, five points behind champions Barcelona and Atletico Madrid, who are level on 35 points.
Pressure has been mounting on Benitez, who is in his first season in charge, particularly since Real were hammered 4-0 at home by Barca in last month's La Liga 'Clasico'.
He also appears to have been blamed by the fans for Real's expulsion from the King's Cup for fielding an ineligible player and has been regularly whistled at the Bernabeu stadium in recent weeks.
Real president Florentino Perez, not known for his patience if the team is underperforming, is standing by Benitez for now but he is widely expected to be discarded unless results do not quickly improve.
A former Valencia, Liverpool, Inter Milan, Chelsea and Napoli manager, Benitez began coaching in Real's youth ranks after his playing career was ended by injury.
"Fortunately I have been working for many years in three different countries and in three important leagues winning titles and I have quite a bit of experience," Benitez said when asked about speculation he will soon be sacked.
"So I just try to do my work and I have also spent many years at Real Madrid," he added. "I follow my own path defending Real Madrid with my work and my respect."
(Writing by Iain Rogers, editing by Justin Palmer)
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