Efimova was alluding to past allegations against Phelps in relation to drugs and alcohol.
The champion swimmer was once photographed appearing to smoke marijuana from a bong, and was arrested for driving under the influence in 2014.
While Phelps was suspended by USA Swimming for both incidents, he has not previously tested positive for performance enhancing drugs.
'Of course I'm not for doping and I've never used it on purpose,' she added.
'But I know there have been very many occasions where people do it because they don't know or because they're stupid or naïve.
'There always should be another chance. When you are driving a car and break a rule, you get only a ticket. You don't lose your licence for life or get put in jail.'
Efimova's Instagram feed shows her in a series of stunning images in the run-up to the Games, showing the athlete posing on the beaches of Miami and El Porto in California, displaying her swimmers' body to her 44,000 followers. She also posted a video of herself wearing a cropped top revealing the word 'Champ' with the caption 'Stay positive'.
And her apparently relaxed frame of mind seemed to work after she claimed a silver medal in the women's 100m breaststroke, despite biting criticism of her doping convictions from her rival Lilly King, who won gold, and US superstar Michael Phelps, who demanded a life ban for those found guilty of taking performance-enhancing drugs.
Efimova tested positive for DHEA in 2013, a banned steroid hormone considered an anabolic agent by the World Anti-Doping Agency. She served a 16-month ban for the substance. Earlier this year she tested positive for meldonium.
Her rival, American swimmer King has made no secret of her disapproval of Efimova, both in interviews and body language.
At an awkward news conference alongside the Russian after the 200m breaststroke, the 19-year-old King said: 'I do think it is a victory for clean sport and just to show that you can do it while... competing clean your whole life.'
However, Efimova remained defiant.
And in an interview published in Russia she added: 'I don't care about them [the taunts from the stands]. Quite the contrary, when people shout nasty things it only makes me angry.
'To those who say that I shouldn't have been at Rio or those who don't like seeing me here I want to say: I was allowed to compete by CAS. I won the case. If anyone if dissatisfied with it, or think that his or her truth weighs more that the CAS's decision, you're welcome to go there and sort it with them.
'I made a mistake once. But there are plenty of cases like this in the world. I was cleared for the second time. And a week before the start, I won the court.'
'I don't really understand the foreign competitors. All athletes should be above politics, but they just watch TV and believe everything they read' - a clear reference to her ban and the fall-out from it.
'I'm really happy, because what has happened to me is unbelievable. I made a mistake once, and I served the punishment. What happened the second time wasn't my fault. I don't know if I should explain in front of everyone'.
'There are those who understand me, these are the people who know me at least a little bit.
'Those who trained with me. It's hurting me when politics start to change us.
'I'd like my competitors especially to show at least a drop of sympathy and understanding of my situation.'
A total of 271 Russian athletes were cleared to take part in the Rio Olympics after the International Olympic Committee (IOC) chose not to hand Russia a blanket ban from the Olympic Games.
