"Due to contract violations, lack of support, unpaid wages, benefits to my players, assistant coaches and myself, I resign as Super Eagles chief coach," he tweeted on his verified account on Friday.
"I feel fortunate, blessed and eternally grateful for having had the honour to play, captain and coach this great nation of ours, Nigeria," added the former World Cup star, who had been in the job since mid-July.
There was no immediate reaction from the Nigerian Football Federation, whose leaders are in Zurich for Friday's FIFA Congress.
Oliseh, who had no previous coaching experience, had helped Nigeria advance to the next phase of World Cup qualification, albeit by an unconvincing aggregate triumph over tiny Swaziland in November.
However, he fared less favourably when in charge of the Nigeria team which performed poorly at last month's African Nations Championship in Rwanda, a tournament for quasi-national sides made up only of home-based players.
The resignation comes less than a month before Nigeria meet Egypt twice in the space of five days in key qualifiers for the 2017 African Nations Cup finals.
The 41-year-old Oliseh, a former midfielder who played at Ajax, Borussia Dortmund and Juventus, featured for the national side between 1993 and 2002.
He won the Nations Cup as a player in 1994 and Olympic gold in Atlanta in 1996 and played at two World Cups.
He had a fiery reputation as a player, missing the 2002 World Cup for disciplinary reasons and was later sacked by Dortmund for allegedly punching a team mate Vahid Hashemian during a loan spell at VfL Bochum.
(Reporting by Mark Gleeson in Cape Town; Editing by John O'Brien)
