Yes and No.
Yes, because racists have jobs in every field/industry and racists will find ways to exploit rules and regulations in the favor of their own personal beliefs, principles, and agenda. The FBI is still a law enforcement agency that recruits people from the criminal justice field who meet higher requirements.
Law enforcement, in general, has a tendency towards being racist depending on what kind of crime they go after. Many crimes are crimes of poverty like there are crimes of passion and crimes of greed, sex crimes, etc. And if an officer has to work under a quota system then even if the system doesn't say "target black people" nor implies it, they will still target black people depending on the area they're in because we're easier targets. Other officers start to pre-judge based on hearing the suspect was black. Part of this is natural. When black people hear about a serial killer our first thought is "probably white dude 25-35" etc. If an officer is based near a poor neighborhood they could be matching crimes to a race so often that a black suspect looks more and more guilty until the crime is being black.
If some of these same cops apply and are accepted by the FBI then they simply bring their racist profiling with them. CIA isn't an internal police force so the criminals they mostly face are probably Arab, according to the region of the world the government is targeting. So for the CIA, they're probably less likely to be racist unless they were already.
The reason why I say no is because I think the FBI is a cross section of America. There are racists within the FBI but without a racist leader they would be too afraid to do things that might expose them because they don't want a more liberal boss finding reasons to get rid of them. That's most jobs. And because the leadership under Trump wasn't decidedly pro-racist, they were investigating Trump and hoping he would lose the election and so forth. If they were racist they would have been quiet booklickers for Trump and they weren't. Not every Trump supporter knew or understood that the MAGA agenda was racist. But if whites were against MAGA it is likely they did, on some level, know and recognize this.
And that's the thing. Time changes things. Many white people have been positively influenced by Black culture to the point that it would be silly for them to be racist when people they idolize are/were black. There is a culture war and racists are getting more desperate because the see that the culture is shifting to be more on our side. And too, a lot of people are being born from mixed parents and multi-racial relationships. And many of them go into law enforcement or military service and get recruited by these organizations. So I know that there are those who believe racist people, places, or groups never change but I don't agree.
I've personally been investigated and questioned by the FBI and I never got the impression that the agent assigned to me was racist. FBI are probably much more the type to "follow the money" in a crime and I think that most often leads them back to white people.