An emergency meeting of the executive committee of the Nigeria Football Federation (NFF) in Abuja asked its technical committee to recommend a replacement on Tuesday, which they will discuss the following day.
"The services of coach Samson Siasia and his technical team have been dispensed with after the unfortunate failure of not qualifying for the Nations Cup," said the NFF statement, signed by board member Effiong Johnson.
The 44-year-old Siasia was a popular choice after he guided Nigeria to the final of the 2005 FIFA U-20 World Cup in the Netherlands and then the final of the 2008 Beijing Olympics.
However, he fell out of favour after his team could only draw 2-2 with Guinea in Abuja earlier this month in a match Nigeria needed to win to stand a chance of qualifying for the Cup of Nations in Gabon and Equatorial Guinea.
Local media have speculated that former Nigeria skipper Stephen Keshi will take over the team in an interim capacity for six months.