Cipriano Cassamá, who on Friday night was declared president of Guinea Bissau before 52 of the 102 deputies of the National Assembly, resigned on Sunday – after just one full day in office.
“I have no security… My life is in danger, the life of my family is in danger, the life of this people is in danger. I cannot accept that, that is why I took this decision,” Cipriano Cassamá told reporters.
Despite not being in the December ballot Mr Cassamá was appointed by parliament, the majority of whose deputies have refused to acknowledge the election victory of the former opposition leader, Umaro Sissoco Embalol.
Mr Embalo who won the presidential run-off refused to wait for the courts to give final judgment before taking over power.
The ruling PAIGC party is contesting that result in the Supreme Court.
Guinea-Bissau has been very unstable since independence, recording four coups and 16 attempted coups since 1974, the last one in 2012.