The Monaco man was not part of his country's squad for Saturday's 2-1 defeat against the United States, having being withdrawn four minutes before half-time in the goalless draw with Greece on Wednesday.
And coach Stephen Keshi has now confirmed that Echiejile will not recover in time to play a part at the tournament in Brazil.
"Doctors have said he will need up to three weeks to recover from the muscle tear, but we don't have that type of time to play with so we have to replace him," said Keshi.
Echiejile will be replaced by winger Ejike Uzoenyi, who was one of seven players dropped from Keshi's provisional squad.
Meanwhile, Chelsea defender Kenneth Omeruo is set to be fit for Nigeria's curtain-raiser against Iran on June 16 after recovering from an ankle injury.
As well as Iran, Nigeria meet Argentina and Bosnia-Herzegovina in Group F.
