Liam Rosenior criticised Paul Tierney after the referee bizarrely gate-crashed Chelsea's pre-match huddle before Saturday's 1-0 defeat against Newcastle.
Newcastle won at Stamford Bridge for the first time in 14 years as Anthony Gordon's 18th-minute strike punished sloppy Chelsea defending.
But the focus after the game was on the curious incident before kick-off when Tierney stood in the centre of a circle of Chelsea players as Blues captain Reece James spoke to his team.
Rosenior said he will contact PGMOL, the referees' body, to seek clarity on why Chelsea's pre-game ritual was disrupted.
Newcastle were due to kick off and Tierney was standing next to the ball near the centre spot, seemingly refusing to move as the home team congregated around him.
"I want to protect my players," said Rosenior after fifth-placed Chelsea's top-four bid suffered a major blow.
"I'm respectful to the game. My players made a decision that they wanted to be around the ball, to respect the ball and show unity and leadership.
"That is not my decision. That is a decision between the leadership group and the team. There is nothing that they're doing with that huddle that is disrespectful to the opposition."
RITUAL HUDDLE
It has become a ritual under Rosenior for Chelsea players to gather in the centre circle before kick-off.
Rosenior has previously said the initiative came from the players, and it has already provoked controversy, with Aston Villa fans booing his side before their recent 4-1 win at Villa Park.
Rosenior has also accused Arsenal's coaching staff of disrespecting his team by encroaching into Chelsea's half during their warm-up at the Emirates Stadium in January.
"Do you know what's amazing?" said Rosenior. "Before the game, we had a meeting with the referee. My assistant goes in. The first thing he talks about is our huddle.
"He said about when I complained about Arsenal being in our half. It wasn't the (Arsenal) goalkeeper coach that was in our half, and people that were at that game at Arsenal know why I said what I said."
Rosenior took another swipe at Tierney by claiming Chelsea should have had a penalty when Cole Palmer went down under a challenge from Nick Woltemade in the second half.
"If Paul had focused more on his job, which was to make the right decision, we'd have a penalty today," he said.
"I don't think anyone can say that Woltemade doesn't kick Cole Palmer down in the box.
"I didn't speak to Paul today, I didn't think it was the right thing. But I'll be speaking to PGMOL. I'll be speaking to the refs. Just trying to get an understanding of what happened."