The former Sierra Leone tactician was dismissed yesterday after 15 months in-charge of Amavubi.
"I am in shock because I have not been told why the Federation has taken this decision," McKinstry said.
"This period has been one of the best in-terms of performance for Rwanda," he added.
The Northern Irishman then led Rwanda to the quarter final stage of the 2016 Africa Nations Championship that they hosted.
He also led the team to the runner-up spot in the 2015 Cecafa Senior Challenge Cup in Addis Ababa, Ethiopia.
"The specific reasons behind the decision have not been made fully clear to me given our performance to date, I am therefore both surprised and disappointed by the announcement today, and that myself and the team will not be able to finish what we started," he said.
The 30-year old coach managed to record 11 wins, two draws and a dozen defeats in the 25 games he was in charge of Rwanda.
According to the Rwanda FA, McKinstry was sacked because he did not achieve some of the targets that had been set for him.
The FA has announced former international Jimmy Mulisa, who had been McKinstry's assistant, as Rwanda's interim coach.