The source cited by the newspaper had said the resignation followed the allegation of not participating in the compulsory National Youth Service Corps (NYSC) and obtaining a certificate that the NYSC have disowned.
It is not clear when she submitted her resignation letter.
The dual Nigerian and British national did not initially comment on the claims, leading to criticism from her opponents.
United States imposes sanctions on Russian, Chinese tech firms over N Korea
Haley and other diplomats claim that Russian Federation pressured the independent monitors to amend the report. Security Council resolutions remains mandatory for all member states - including Russian Federation ".
However in a statement, she said she felt bound to resign after the investigation result became known. Until I hear from her, my assumption is that it's not true. She also instituted a whistle-blower policy and helped push reforms to boost Nigeria's tax collection to increase non-oil revenue as the West African nation seeks to wean itself off oil.
The presidency approved that the minister of state for budget and national planning, Zainab Ahmed, would oversee the Finance Ministry with immediate effect, it said on its official Twitter account.
Under the scheme introduced in the early 1970s to promote unity among Nigeria's multi-ethnic groups following a 30-month brutal civil war, graduates younger than 30 are expected to serve the nation for one year.