Aitor Karanka did not take training at Middlesbrough on Saturday morning and will not be in charge for Sunday's trip to Charlton, the club have announced.
Karanka is understood to have left the Sky Bet Championship club's training ground unexpectedly on Friday following a meeting.
The Spaniard's dramatic departure triggered a series of rumours, and promotion-chasing Boro have now released a statement confirming Steve Agnew will be take charge at The Valley but without commenting on Karanka's future.
It read: "Middlesbrough Football Club can confirm that Aitor Karanka did not take training on Saturday morning.
"Assistant Head Coach Steve Agnew will take charge of the team for Sunday's fixture at Charlton Athletic.
"We appreciate supporters will want to know further details, but at this time the club cannot make any further comment and is solely focused on Sunday's game at The Valley."
Middlesbrough head into the weekend sitting in second place in the Championship table, four points behind leaders Burnley with a game in hand, and two points clear of the chasing pack.
However, they have won just three of their last 10 games and taken 12 points from a possible 30 to surrender what was once a commanding lead.
There is also an ongoing debate over Karanka's use of ?9million January signing Jordan Rhodes, who has started just four times in eight appearances and scored a single goal since his arrival from Blackburn.