Following accusations of state-sponsored doping, 118 competitors of the 389-strong Russian team
were banned ahead of the start of the Olympic Games, due to a long running doping scandal that has overshadowed Rio 2016.
"I think just with what has happened over the last year and the whole Russia situation, it has truly shocked so many people," 30-year-old Ennis-Hill told CNN's Amanda Davies.
"I think although a lot of athletes were aware that something wasn't quite right, we didn't realize it was on this scale. For the athletes that train so hard, train day in and day out and come to compete as clean athletes, it's just really frustrating to know that some people aren't doing it properly," added Ennis-Hill.
"I suppose now more people feel like voicing their opinion which is really good for the sport and hopefully we can start making progress to clear up the whole sport in its entirety."
Before the Olympic Games began, Alexander Zhukov, president of the Russian Olympics Committee, told reporters that no team has been drug tested as much as Russia.
"Each and every sportsperson was checked and tested, and the international federations checked them and they concluded and made the decision that there were negative ... a huge amount of negative test results that indicates that the huge amount of sportsmen are completely clean."
As she prepares for the start of the heptathlon Friday, Olympic champion Ennis Hill says she won't be distracted by the suspicions surrounding some of her competitors when she takes to the blocks for the 100m.
"As an athlete now you've got to line up, you don't think about that. You've got to focus on yourself and your performances and just know what you can do to get out of your event. We need to put trust in the federations and make sure that they make a change and clean our sport up.
She added: "I've been in athletics for so long and it is a great sport. There are some amazing performances, inspiring in so many ways and for me, I want the world to see how amazing our athletics is. What better show than the Olympics."
At the 2011 World Championships in Daegu, Tatyana Chernova pipped Ennis Hill to gold, but a sample provided by the Russian athlete back in 2009 was then retested and the 2008 Olympic bronze medalist was eventually given a retrospective two-year ban from the sport.
Asked whether she had any sympathy for Chernova, Ennis-Hill explained her overwhelming feeling was one of disappointment
"I mean it's very difficult to say that. I am an athlete that trains hard and works really hard and I was denied a World Championship gold medal and that was going into a big year for me as well with the Olympics.
"Although I was happy to achieve a medal on a world stage I was really disappointed because I felt like I was in the best shape. I thought I was doing really well and going into an Olympic year in a really positive position and then missed out on that gold medal," Ennis-Hill said.
"I know so many athletes that have worked hard, had injuries and setbacks and missed out on medals through people cheating so it's very hard for me to make that comment."
In February, the Court of Arbitration of Sport said that it was handling a athletic blood passport case belonging to Chernova and middle distance runner Kristina Ugarova.
"These cases will again be handled by the CAS as a first instance decision making authority. However, for both of these athletes, this constitutes a second anti doping rule violation as CAS already has pending arbitration procedures with them relating to separate matters, although these are suspended until the outcome of the ABP cases is known."