Darren Ferguson has said controversial comments he made after Doncaster's 1-1 draw against Plymouth were "tongue-in-cheek," stressing that he does not advocate violence against officials.
Rovers were denied a last-minute penalty at the Keepmoat Stadium when James Coppinger was felled in the box, promoting Doncaster boss Ferguson to launch a scathing attack on referee Andy Baines.
The 45-year-old was asked by BBC Radio Sheffield how he would like the Football Association to address the issue and said: "The referees are part-time and the standard is appalling. Their fitness levels are a disgrace, I've had enough of it.
"What can I do? Shoot them, it would be a good idea."
The former Peterborough and Preston boss moved to resolve the matter on Sunday as he apologised for his remarks.
He said: "When asked after the game what I personally could do to see to raise standards, I said: 'What can I do? Shoot them?'
"Although clear to everyone in the room that my comment was a tongue-in-cheek response, it is worth clarifying my comments were borne out of frustration and I absolutely do not advocate violence against officials.
"I am sorry for that comment and regret the wording but, as was clear from my postmatch comments, I felt the referee got some decisions wrong at key moments in the game.
"Referees have a tough job and I have a lot of respect for the challenges they face, but I would like to see more done to raise standards across the board and give them the best chance of getting decisions right."