Barnsley say they are "shocked" by manager Paul Heckingbottom's departure to Leeds - which came just three days after he signed a new rolling contract.
The club expressed their "thorough disappointment" following the completion of what they described as a "successful transfer window".
Leeds appointed Heckingbottom as their new head coach following Sunday's departure of Thomas Christiansen.
The 40-year-old has agreed a deal until the end of 2018-19.
"The club are shocked at Paul Heckingbottom's desire to leave, having agreed a new contract last week following the completion of the transfer window, where the directors worked tirelessly along with Paul to secure their targets, resulting in a successful window," the statement said.
"This left the club optimistic in a turnaround in form and a strong end to the 2017-18 campaign as we battle to retain our position in the league."
Paul Harsley will temporarily take charge, with the statement adding the board "fully trusts him."
Heckingbottom guided Barnsley to promotion via the League One play-offs and won the Johnstone's Paint Trophy in 2015-16, but leaves them just one point above the relegation zone.
The move comes exactly two years to the day since Lee Johnson left the Barnsley job to take over at Bristol City and Heckingbottom took charge.
BBC Radio Leeds reports the Whites paid £500,000 to activate a release clause in Heckingbottom's Barnsley contract, which he only signed on Friday.
Leeds, who dismissed 44-year-old Dane Christiansen after just eight months and have not won since Boxing Day, will host Barnsley in the league on 21 April.
Heckingbottom's new club are seven points below the play-offs in 10th, while Barnsley are 21st.
He becomes Leeds' ninth different first-team boss since 2014.