Saturday's 1-1 draw with Coca-Cola Championship winners Reading confirmed Sheffield United's promotion and consigned Leeds to the play-offs.
Leeds are now winless in seven matches but of far greater concern to Blackwell is a virus which is believed to be emanating from the club's Thorp Arch training ground.
It has so far affected skipper Paul Butler, Gary Kelly, Danny Graham, Gylfi Einarsson and Robbie Blake.
"We've got a virus in the camp which has swept through it and we lost Robbie Blake at 11 o'clock on Saturday morning," Blackwell said.
"I'm losing players just prior to games and we've got to somehow assess where the virus is coming from.
"It's lasting for a week and a half so we've got a problem here and we don't need that at this point in the season."
Striker Blake was the last player to leave Thorp Arch on Friday after training and Blackwell added: "We've got to try and work out the last connection Robbie Blake had and trace it back to that.
"It's flu-like symptoms for two or three days and then it turns into a virus.
"I'm waiting every morning to see who is going to ring in next to say they're not going to be fit.
"It could be contagious just by mixing together. It could be lingering around the training ground area because it's a hot, humid place."
Leeds had gone six hours without scoring a goal before Rob Hulse's predatory strike, his 13th of the season, shortly after the interval.
However, Royals substitute Stephen Hunt bundled home an 85th-minute equaliser to ensure no side has taken four points off the champions this season.
Reading are now six points away from the record of 105 points, set by Sunderland in the 1998-9 season, with three matches left.
For Leeds the play-offs beckon, and Reading goalscorer Hunt believes there are considerable grounds for optimism at Elland Road.
He said: "I had a look around the stadium and the top tier on one of the stands was empty.
"If that's full, then crikey, anyone coming to Leeds United in the first or second leg of the play-offs will find it very difficult.
"It's a big ground and an intimidating place, so Leeds have a great chance. Whoever deals with the pressure best will go up."