In a statement, the office of the Director of National Intelligence said the bulk of telephone data - the subject of leaks by former intelligence contractor Edward Snowden which shocked many in the US and abroad - would be destroyed "as soon as possible" to comply with a law passed by congress in early June.
But it added that "for data integrity purposes", NSA will allow technical personnel to continue to have access to the metadata for an additional three months after the program ends on November 29.
Barack Obama's administration signed a law on June 2 that outlaws the bulk collection of American's telephone records, instead requiring intelligence agencies to collect targeted records from telephone companies.
The USA Freedom Act gave the NSA a six-month grace period.
The controversial programme, exposed by former NSA contractor Edward Snowden, was rocked in May by an appeals court ruling that the USA Patriot Act had never authorized the NSA to collect Americans' phone records in bulk.
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The NSA programme collects and analyses data about Americans' phone calls, such as the number dialled, and the time and length of the call, but not the calls' actual content.
The Freedom Act requires companies such as Verizon Communications Inc and AT&T Inc, to collect and store telephone records the same way that they do now for billing purposes.
- with Agencies
