The 33-year-old Johnson will make a world farewell tour this year where he will only run in relays and non-championship distances.
The world record holder for the 200 and 400m had hoped to run in the 4x400m without first competing in the US Championships.
But his plans were dented by chairman of the US men's track and field committee John Chaplin.
Speaking after a Track and Field board of directors' conference, he said every athlete hoping to compete in the worlds "has to go to the (US) meet and run one round in one event".
The conference discussed altering the long-standing rule that all athletes wishing to represent the United States at an Olympic Games or world championships had to compete in the national championships.
The 33-year-old Johnson will make a world farewell tour this year where he will only run in relays and non-championship distances.
But he had been hoping to end his illustrious international athletics career in Edmonton and to capture his 10th world title.
"I'm not going to say it wouldn't be fun for me," said the five time Olympic gold medallist.
"But it's not a disappointment for me because I'm still doing things that are important to me.
"I'll still be at the world championships signing autographs and doing other things for fans.
"I never asked for anything special, and I'm never going to. I don't want any controversy to take away from what I want to do this year."