John Senior has addressed the controversy after more than 2,000 people signed a petition to have Tom Clark MBE reinstated.
Mr Clark was sacked after an investigation by the charity found that he had led an "unauthorised" training exercises.
He had been with Scarborough RNLI for more than 30 years.
In a statement, Mr Senior said: "Since Scarborough lifeboat station's coxswain Tom Clark was permanently stood down, a lot of anger has been directed towards the station and the RNLI.We would like to make it clear that the decision to suspend and then stand down Tom was not taken locally.
"Following his suspension in October, many of the crew and station personnel have made their views clear to the RNLI management and we at Scarborough lifeboat station acknowledge the anger felt by many people in the town and elsewhere.
"However, we ask that people respect that we are all volunteers and that our lifeboatt crews are still working hard to do what we do best - launch our lifeboats and save lives at sea."