Stephen Baxter says he spoke with referee Mervyn Smyth and wished him all the best for the future after the official quit following the County Antrim Shield final last week.
The Crues boss was critical of Smyth's decision to show Paul Heatley a red card after his side lost 3-1 to Linfield at the Ballymena Showgrounds.
"I spoke with Mervyn Smyth and I was disappointed with headlines saying Baxter blasts media after the final," said the Crues boss.
"I did not speak to Mervyn around the Paul Heatley situation. I was asked a question regarding another possible red card and that's where this has come from. Mervyn Smyth is a guy I respect and someone I have known for a long time. He is a wonderful guy and if I had something to dispute with a referee I would have a word with them in the right manner.
"Mervyn Smyth did not stop refereeing on the back of my comment, I can assure you of that. I wished him well in whatever he does, he's a really good fella."
Irish League refs have come in for stinging criticism and Baxter feels that everyone in the game should be striving for better performances, including the men in black.
"Referees are very pivotal to the game but their job is to officiate the rules, they aren't the centre of attraction - the players are," he added.
"I'm not or the coaching staff, the players are the people who put their body on the line in any sport and we pay to watch them.
"I have been a supporter of referees and gone out of my way to talk to them or in some cases write to them to encourage them but of course I will dispute decisions as that's what the game is about, there's a passion in asking for decisions and we should have the right relationships to talk about these issues but referees have a big responsibility to work on their performance and to be the best that they can be.
"I get the criticism of referees as decisions have major implications for teams. It's a tough scenario and referees carry that weight of responsibility and that's why I'll support them.
"With regard to the Paul Heatley sending off, we could have appealed the decision and we are a bit disappointed that it has not been rescinded. He will suffer the consequences of a two-game ban and had we appealed it we could have lost Paul for big games in the weeks ahead."
Although the disappointment of the Shield final will linger a little longer at Seaview, Baxter was lifted by his side's 2-1 victory over Ballymena United on Saturday.
Tony Kane's stunning 78th-minute free-kick threatened a comeback after first-half strikes from Gavin Whyte and David Cushley but the champions netted another big three points en route to what they hope will be a third consecutive league title.
Winger Whyte, the subject of bids last month from Dundee United, returned from a hamstring injury to give another demonstration of his attacking class.
"In my first season there was a lot of talk and it went to my head a bit," admitted the man from the Markets who has taken his goal tally to 10 for the season. "I'm not like that anymore. If a move happens it happens, if it doesn't it doesn't. I'm happy playing here and we'll see what happens. I can see things from the club's point of view, they want me to help them win a league title and I want that too.
"I'm not thinking about it, I'm just enjoying my football."
Baxter was thrilled to see Whyte back doing what he does best. He added: "We kept him informed about all the speculation. There was a hamstring injury and he didn't play for two weeks but he showed here how good a player he is and he has the potential to really kick on and become a super, super player.
"But he loves being with us and the camaraderie, he wants a third title and I said to him keep playing well and there will not be one, but 10 teams looking at you."