It is understood the Spaniard reported for duty on Saturday morning ready to take training ahead of Sunday's Sky Bet Championship trip to Charlton, a day after walking out following a stormy meeting with his players.
Sources close to Karanka, who has previously found himself at odds with former assistant Craig Hignett and midfielder Albert Adomah during his 28-month reign, claim he arrived ready to apologise for his part in the disagreement and smooth things over.
However, he did not lead training and the club later released a statement confirming he will not be in charge of the team at the Valley.
The statement said: "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."
The Teessiders went into the weekend sitting in second place in the 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, and there have been rumours of unrest in recent weeks.
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.