Oliseh, who was just eight months into a three-year contract, said he quit because he did not enjoy the support of the Nigeria Football Federation (NFF).
he wrote on Twitter in the early hours of Friday.
The man he replaced in July 2015, Stephen Keshi, had previously complained of unpaid wages and was later paid the arrears by Nigeria's presidency in 2013.
Players have also protested in the past about unpaid bonuses.
Oliseh's resignation comes just a month before a crunch Africa Cup of Nations qualifier against Egypt in the northern city of Kaduna with the return leg two days later in Cairo.
Egypt are seven-times winners of the tournament but Oliseh said he has been unable to travel to Europe to assess Nigerian players to pick his squad for the double-header.
NFF general-secretary Mohammed Sanusi, in Zurich for Friday's vote to elect a new president of the sport's world governing body FIFA, confirmed the federation had received Oliseh's resignation.
"We will meet and decide on what next," he added.
- 'Abandoning the ship' -
With Oliseh's resignation, Nigeria face an uphill battle to defend the title they won in 2013 in South Africa and after failing to qualify for last year's finals.
Egypt head Group G with six points after two matches, with the Super Eagles second on four points. Only the overall group winners are guaranteed automatic qualification to the 2017 finals in Gabon.
Former national team official Ben Alaiya said 41-year-old Oliseh's resignation has further compromised the country's chances of getting through.
"It's a shock. He should not have quit, it was like abandoning the ship in the middle of the sea. It was a big slap to 180 million Nigerians," he said.
Former Nigeria international Dosu Joseph said the NFF must move quickly to appoint a successor to stay on track for Gabon 2017.
"Many of us saw this coming but we now need to move forward because we have beat Egypt at least at home or else kiss goodbye to the Nations Cup," he warned.
"The NFF must now sit up for the matches against Egypt because it will be a disaster if we failed again to qualify for the Nations Cup."
Oliseh has had a tense relationship with the NFF since Nigeria failed to go past the group stage of the recent African Nations Championships in Rwanda.
He vented his frustration in a YouTube video earlier this month, attacking critics who wanted him sacked, but later apologised, while sports minister Solomon Dalgun backed him to stay on.
- Likely contenders -
Former Nigeria coaches Shaibu Amodu and Samson Siasia are the early front-runners as caretaker coaches before a substantive coach is named.
The experienced Amodu has handled the Super Eagles before, securing qualification to the 2002 and 2014 World Cups. He is currently the NFF technical director.
Siasia served a short stint as national team coach between 2010 and 2011.
He was sacked after Nigeria failed to reach the 2012 Nations Cup finals in Gabon and Equatorial Guinea.
Emmanuel Amuneke, who has been promoted to the Under-20 national team after he led the Golden Eaglets to a fifth FIFA U17 World Cup in November, could also be considered.
But it is expected Salisu Yusuf, who has assisted Oliseh, will stay on to be a link between the coach and the team his former boss was trying to build before he threw in the towel.