"The scans revealed that he has suffered a recurrence of a stress fracture of his right elbow."
Archer underwent operation in May to remove a bone fragment from his elbow and was left out of England's two-test series in June against New Zealand, which they lost 1-0.
The 26-year-old was also excluded from England's squad for the opening two tests against India and the ECB said he will now miss the rest of the series.
"As part of his return-to-bowling programme, he became aware of increasing discomfort in his elbow during matches for Sussex in the Vitality Blast and a 50-over friendly against Oxfordshire," the ECB added.
"The operation is not related to the stress fracture that sidelined the player previously. He will now spend time on an extended break from cricket before returning for a medical review in early autumn."
Barbados-born Archer has been plagued by the injury since early 2020 and it kept him out of this year's Indian Premier League.
The T20 World Cup is scheduled to be held from 17 October-14 November in the United Arab Emirates and Oman. The five-test Ashes series is scheduled to begin on 8 December in Brisbane.