Nigeria take on Ghana on August 9 at Watford’s Vicarage Road Stadium.
The Fulham midfielder opted out of playing for the Super Eagles in a late substitution against the Black Stars as John Mikel Obi cannot play for Siasia's team due to injury.
In what could have been Etuhu’s first cap under Samson Siasia, the midfielder turned down the opportunity, saying he will not play for the manager.
"Etuhu has refused to join the squad for the Ghana game as a late replacement for some of the players who will now not be there because of visa issues," MTNFootball quoted an unnamed team official.
"No one really knows why he has refused but he said he will not play for Nigeria under Siasia."
Etuhu has been overlooked by the coach since he missed a call up early in the year due to an injury.
Nigeria are faced with injuries to key players as well as visa denials to other members of the team, including goalkeeper Vincent Enyeama, striker Ekigho Ehiosun, midfielder Fegor Ogude and defender Efe Ambrose.
The match against the Black Stars is aimed at preparing them for their African Cup of Nations qualifier against Madagascar in September.