The Tannadice chairman cast most of the blame at the players after United slipped 13 points adrift at the foot of the Ladbrokes Premiership table, although he has admitted some culpability as a board member.
United lost 3-0 at home to Motherwell, who were second bottom before the game, and manager Mixu Paatelainen admitted he was baffled by their "flat" display on Tuesday night
In a statement issued on the club's official website, Thompson said: "As chairman of the club, I would like apologise to all Dundee United supporters for the abysmal performance last night against Motherwell.
"The current position at the bottom of the Ladbrokes Premiership is wholly unacceptable
It is not where Dundee United should be under any circumstance.
"The board and myself have made certain decisions in the last eighteen months which in hindsight were incorrect but were made for the greater good of the club and with the ambition of maintaining our position at the top of Scottish football, something we have done successfully for the last eight years.
"This included supporting a playing squad that commands the third highest wage bill in the Ladbrokes Premiership.
"However, we have failed miserably on the pitch with only three wins in 25 league matches and an early exit from the League Cup
Performances such as last night simply cannot be tolerated.
"The current playing squad now have thirteen matches to preserve the club's Premiership status and redeem their own professional reputations."
Source : PA