The NAACP says that for several months it has watched a pattern of disturbing incidents reported by black passengers.
The airline said it was disappointed by this warning.
In the advisory, the NAACP listed four incidents in which black passengers said they were discriminated against by AA employees.
Johnson said the NAACP's "growing list of incidents. involves behavior that can not be dismissed as normal or random".
In another instance, American Airlines booted a black male passenger from a North Carolina-bound flight for responding to "disrespectful comments directed towards him by two unruly white passengers".
The second incident involved a complaint from a black passenger who said she was bumped from first class to coach but her white friend, whose ticket she also booked, wasn't.
During another incident, Tamika Mallory, co-chairwoman of the Women's March on Washington, was removed from a New York-bound flight when she complained about her seat being reassigned without her consent.
The group said it had issued a "national travel advisory" in response to what it described as "disrespectful, discriminatory or unsafe conditions" for African Americans traveling on the world's largest airline.
In that message Parker expressed disappointment at the NAACP travel warning and wrote, "We do not and will not tolerate discrimination of any kind".
American Airlines issued a statement saying that it serves customers of all backgrounds and itself has a diverse group of employees. "I was singled out, I was disrespected, and he was trying to intimidate me", she told the Daily News after the incident.
'We take these allegations seriously, and we are in the process of reaching out to our colleagues in Miami, as well as Ms. Mallory, to obtain additional information on what transpired during the boarding process, ' American Airlines added.
Unlike when the NAACP issued an advisory in June for black Americans traveling in the state of Missouri, Tuesday's announcement did not include any qualitative data to support a targeting of black Americans.
But earlier this month, national co-chair of the Women's March movement Tamika D. Mallory was kicked off a flight traveling from Miami to NY. The civil rights organization's advisory calls for African-American travelers to be cautious of traveling or utilizing resources with American Airlines. "Change has to happen, it has to start somewhere, if we just keep funding them, keep giving them our money, they're just going to keep treating us any type of way", said Christina Tunstall, a student at San Jose State University.
"The NAACP deplores such alarming behavior on the part of airline personnel, and we are aware of these incidents only because the passengers involved knew their rights, knew to speak up and exercised the courage to do so promptly", read the statement.