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She is, however, expected to continue in her post for another two weeks at least, the spokesman said.
Chamberlin, a divorcee with two teenage daughters, has been in Pakistan for less than a year.
She has publicly expressed concern about the security scenario in Pakistan, especially after the September 11 terror attacks in the US.
When the US launched its campaign in Afghanistan last year to capture Saudi extremist Osama bin Laden and destroy his Al Qaeda outfit, families of US diplomats in Pakistan had been evacuated.
Though they returned in February, they got a shock in the form of the March 17 attack on a church in Islamabad.
Five persons, including an employee of the US embassy and her teenage daughter, were killed in the incident.
Wednesday's attack, in which 11 French defence experts were among 14 persons killed in a suicide attack in Karachi, was another reminder of the grim security scenario for Westerners in Pakistan.
Chamberlin had served as US ambassador in Malaysia and Laos before being posted to Pakistan.
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