The former governor general was criticized recently after Montreal La Presse reported that her personal trips on the aircraft cost taxpayers more than $500,000.
Jean told The Canadian Press on Friday she never had a say in the matter because the RCMP's strict security protocols mandated her to use the airplanes.
She added that the country was at war in Afghanistan at the time and she was highly visible as commander-in-chief of the Canadian Forces.
"If you follow the logic of some terrorist organizations, I could certainly be a person targeted by them because when they hit — they want to do it in a very spectacular manner," said Jean, who seemed eager to address the matter when asked about it in a telephone interview from Ottawa.
"They did not want to take that risk. And this is the world today, I'm sorry. If people want to contest that, well they have to contest the RCMP's work."
The newspaper reported that Jean's eight personal flights on government aircraft cost taxpayers a total of $553,756 between January 2006 and September 2010, the month she left the post.
According to the report, Jean, her husband and her daughter took government-funded flights during that period to destinations such as Jamaica, Mexico, Barbados and to their second home in France.
Jean, who was sworn in as the Queen's representative to Canada in September 2005, underscored that she always paid for the vacations out of her own pocket, but didn't have an option when it came to the transportation.
She said she was told travelling on commercial flights could have also put the lives of others in danger.
Jean recalled how bodyguards followed her everywhere and the Mounties even worked with local police in the countries she visited to ensure her safety. The RCMP also swept her accommodations prior to her arrival for possible threats and installed cameras at her cottage.
"For five years, I put my privacy aside," she said. "I had to be accompanied all the time for security reasons. No matter where I was going."
In the interview, Jean brushed aside another monarchy-related question that has made recent headlines: the Conservative government's decision to display the Queen's portrait in Canadian embassies.
"Well, I think you should ask the current Governor General and I think you should ask, certainly, the government on it because it's a decision that belongs to the government — what they hang, what they don't hang," said Jean, who was more interested in discussing the importance of safeguarding the position of Canada's governor general.
Jean pointed out that other countries take similar steps to protect their prominent figures — particularly those with the powers to carry out the duties of their head of state.
"Why don't we understand that for Canada, for ourselves?" Jean asked.
"When some terrorist organizations decide to target, no matter where you are, what you are doing, they will do it. They (the RCMP) did not want to take that risk."
Jean, who now serves as a special envoy for the United Nations in Haiti, learned about the controversy around her private trips while on a week-long visit to the impoverished Caribbean nation.
The Haitian-born Jean has been working in the country on projects such as promoting cultural tourism and rebuilding the struggling education system. She estimates that 500,000 Haitian kids who should be in school are, in fact, not.
She twice met with Haitian President Michel Martelly during a week-long stay in the country, where she witnessed signs of progress in an area still struggling after the devastating January 2010 earthquake.
Jean, who now only flies on commercial airlines, said she's travelled in recent weeks to regions such as Europe to appeal for more assistance on Haiti's behalf. She wants to ensure its needs stay on the international radar.
"Every time a crisis happens elsewhere the attention for Haiti diminishes," she said.
"I wanted to make sure that the international community would continue with its commitment towards Haiti."