Emeka Inyama, chairman of the NFF's Media and Publicity Committee, said news of the incident came to the Federation as a rude shock.
"It is a very unfortunate, very sad incident. Gbenga Okunnowo served this country meritoriously at both junior and senior levels, and played for such a revered club as FC Barcelona. He does not deserve what has happened to him.
"We grieve with him and his family at this sorrowful period. It is lamentable."
It was reported that fire from a PHCN building around 1am in the night spread to the duplex of the former international defender, and destroyed the building, including valuable items such as international passports, European residency papers and money.
Okunnowo represented Nigeria at both junior and senior levels, captaining the U-20 Team, Flying Eagles during the FIFA World Youth Championship that Nigeria hosted in 1999, and later played for FC Barcelona in Spain and SC Benfica in Portugal.
He returned to Nigeria last year and only a few weeks ago, mutually agreed with Sunshine Stars FC of Akure to cancel his contract.