World football's governing body said the decision followed a bid by the Minister of Sports to restart the league without relegations, pressure to oust the Nigerian Football Federation's acting general secretary and court action barring elected members of the federation's executive committee.
"The FIFA Emergency Committee decided today, 4 October 2010, to suspend the Nigeria Football Federation (NFF) with immediate effect on account of government interference," FIFA said in a statement.
"During the period of suspension, the NFF will not be able to be represented in any regional, continental or international competitions, including at club level, and also not in friendly matches," it added.
Nigeria's government sought to ban the national side from playing shortly after the African footballing powerhouse bowed out of the continent's first World Cup in South Africa in the group stage with just one point.
The two-year ban was lifted on July 5 after FIFA imposed a deadline to stop political interference.
But several footballing executives were sacked and President Goodluck Jonathan also ordered an investigation into how the funds allocated for the World Cup team were used.
A corruption case brought against four former football federation officials was due to resume on Tuesday after being adjourned last month.
Nigeria's anti-graft agency has accused former NFF president Sani Lulu, vice-president Amanze Uchegbulam, secretary-general Bolaji Ojo-Oba and chairman of the NFF technical committee, Taiwo Ogunjobi, of 10 counts of corruption.
The charges against the officials include mismanaging a World Cup budget of 900 million naira (about six million US dollars) and paying out allowances to unauthorised officials totalling over 800,000 US dollars.
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