His position was thrown into serious doubt at the weekend when the promotion hopefuls disclosed he would not be in charge for Sunday's fixture at Charlton Athletic, which they lost 2-0.
"Middlesbrough can confirm that head coach Aitor Karanka will be resuming first team duties with immediate effect," the club said in a statement on Monday.
"We have 10 games left this season and as a club we are fully focussed on what remains of our Championship campaign."
British media reported last week that Karanka, former assistant to Jose Mourinho during the Portuguese's spell in charge of Real Madrid, was involved in a row at a team meeting.
Middlesbrough are second in the table, seven points behind Burnley but with a game in hand on the leaders. The top two are automatically promoted to the Premier League.
(Writing by Tony Jimenez; Editing by Ken Ferris)
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